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The default humanoid is more believable than you think

A lifeform does not have to be humanoid to be intelligent, but being generally humanoid helps a LOT with tool use. On Earth, we have a few species of cephalopods, cetaceans, and avians that evolved advanced intelligence well before our human ancestors did, but they don't have the body plans to form an advanced civilization; so, thier intelligence seems to have capped at about where hominids were in the early stone age, while humanoids were able to keep going.

Features you should consider for all of your aliens are:

1. Bilateral symmetry appears to be universally advantageous for complex organisms. There are very few examples of non-bilateral life on Earth that is more advanced than a starfish; so, assume this to be common elsewhere too. It also means that all of the below assertions should assume an even number of arms, legs, etc. Though throwing in 1 or 2 radially symmetrical races could be believable.
2. If you live in an aquatic environment, you can be smart, but never develop fire which means you will never develop chemistry, metallurgy, or ceramics or any of the other things that helped humans get out of the stone age. This means that nearly all of your aliens should be terrestrial or amphibious, and come from an oxygen rich planet.
3. If you don't have something like fingers, then you will be very dexterity limited in your tool use. Again, this caps you at a very primitive state. So, all of your aliens should have something like hands with multiple fingers. Something more tentacle like works too, but don't give them suckers because those require an aquatic environment to form a good seal.
4. If you have less than 2 arms, you will have a hard time manipulating objects against each-other and if you have more than 2 primary arms, then your arms will be strength limited compared to your size. So, most of your aliens should have 2 main arms, plus maybe 2-4 smaller arms or arms that second as feet. More than 6 arms with no fingers might happen too, where the arms work together for grasping, but expect that to be more rare since it wastes a lot more body mass on the extra appendages compared to 1 arm with many fingers
5. If your head can't see what your hands are doing, it limits your ability to use tools. So all aliens should have eyes (or comparable sensory organs) that can comfortably face whatever your alien is touching for hours on end. A vision like sense is also very helpful for developing reading and writing though not absolutely necessary. These organs should also be in a head containing the brain and all of your other major sensory organs since this improves processing and reaction time by putting them all closer to the brain. This is seen in nearly all complex life forms; so, assume aliens will be similar. Secondary neural ganglions may exist throughout the rest of the body to improve motor control like an octopus does, but the actually sensory processing and executive thought parts of the nervous system should be in a head.
6. If you can't locomote while carrying a heavy load, then this limits your ability to use large tools and to construct buildings, or even to gather wood for a fire. This is where the upright body plan of the humanoid really shines because humans can lift and move things very well. Centaur or Naga like body plans may work well too. This will make body types without skeletons of any sort much more rare though because an upright body plan requires structure.
7. Avoid really good natural defenses. A tiger or a chameleon would have very little reason stop and make a spear, even if they could, So body designs that are just a little bit helpless without weapons and tools puts the evolutionary pressure on to develop weapon and tool use. Don't get me wrong: claws, fangs, venom, and active camouflage are are perfectly reasonable adaptations to have... just don't make them too perfect of versions of these adaptations.

Areas where you should see a lot of variance:

1. Color and skin type. Fur, feather, scales, shells, exoskeletons, and others will all be evolved to deal with each alien's native environment and ancestorial lineage. So, any choice is as believable as another. That said, remember that any alien that does not see in the visual light spectrum will likely be black, white, or clear skinned if it comes from a planet where being seen by human like eyes is a not issue. Or the inverse, they could be very ornately patterned (like parrots) if they live where only themselves and few other animals can see in the visible light spectrum.
2. Sensory Organs. Human eyes, ears, mouths, and noses don't even look that much like some other mammals, much less animals in general. Alien sensory organs may be shaped very differently than humans, and even work by other mechanisms all together, but still plan to slap most of them into a head, and have some analogue for sight and feeling because they need to be able to have a good sense of what they are working on when tooling.
3. Digestive organs. While it should be true that your aliens will typically have a way to consume food and expel waste, the organs for this can come in all shapes an sizes and these have no baring on how smart or tool using your alien can be. Some aliens may throw up thier waste instead of having a specialized anus. Some may have sideways mouths, mandibles, proboscis, fangs, tusks, beaks, etc. Some might even be primary producers and need to sit in a tanning bed or a nutrient bath to "eat"... though I expect this to be more rare due to the energy requirements of being a tool user.
4. Legs and Feet. While hands are a pretty specific requirement, there is a lot more room for variance with the feet. This part of the body could be pretty much any number of legs with any number of joints. It could even be serpentine or something completely alien. As long as your alien can move around while holding something kind of heavy, its bottom section should be fine.
5. Size. The human brain is far from the most size efficient an organic brain can be. Even using Earth base biology, a bird brain the size of an orange could out perform the human brain; so, expect some aliens to be as small as a medium sized dog whereas others could be the size of an elephant.

Conclusion

While all these rules do not mean that the default should be exactly humanoid, it does mean that every advanced civilization should have a lot of common features with humanoids. Considering the specifications above, I think making ~25% of your aliens truly humanoid (2 arms, 2 legs, phalanges, etc.) is a good idea, but all of your advanced aliens should be "effectively" humanoid in terms of what thier body plans can get accomplished, even if they get there by different means.

In short, your universe probably has thousands of intelligent races, but only the 20 or 30 with good body plans and environments will develop past the stone age. So what they see as 1-in-4 intelligent races being humanoid is actually more like a 1 in 1000 kind of thing... it just takes a lot more than intelligence to cross the threshold into forming an advanced civilization.

The OP said in comments on another question "In my world, the whole plot is 'its a mystery' with the humanoid species all trying to put forward their own theories for why it is" actually works well with this because there will be a lot of debate about what constitutes intelligent life. Here on Earth, we can't decide if a whale is more or less smart than a human, and we've lived along side them for thousands of years; so, any alien that does not have a strong interest in xenobiology will likely dismiss most intelligent life forms as simple animals. So, while the Xyphlonians might claim there is no mystery because only 1 in a million sentient being are humanoids because they have a very broad idea of intelligence, the Droxians might say that there is no mystery because the Droxians are the only intelligent species in the whole universe because even those other animals that can make spaceships can't comprehend some manner of thinking that is uniquely Droxian; so, they are just animals that make stuff no different than beavers or ants. The "mystery" only exists for those in the middle like us Humans that find space flight to be something special. In reality, it's just a very specific niche; so, convergent evolution will play a big part in what it takes to fill that niche.