Yes, they will have unique skills and even knowledge.
Now, with that said...
Transcended people may reach standards faster than us. And in time they may reach a very similar mindset and even similar skills. But their individual base will always be there, otherwise they aren't different individuals any more, and just components of a bigger single entity. I will elaborate.
We interact with the computers in a very isolated way. We have to move our bodies to operate some kind of input device, and a complex system of layers of hardware and software is required in the middle.
I believe that digitized people still require some level of isolation to prevent malfunctioning and data corruption. So there will be some kind of software driver and probably sandboxing. For example, those people brains are already educated to do something with the signals coming from their senses. The most efficient way is to translate everything to visual, audio, tact, so they can use what they already know. In a sense, they are still isolated, as they accept inputs in fixed formats.
Can they evolve from their biological emulated starting point and begin accept other formats? Probably. But for the current state of their synapses to be useful, you have to emulate senses at least at the beginning. The being can then evolve from there. If your setting already provided the time required for such evolution, then it is believable. You don't have biological beings, but that alone doesn't guarantee there was enough time to digital evolution. Adjust the details for the outcome you want.
When you transcend, what you upload is an image of the current state of your neurons synapses. This allows you to retain everything, knowledge, personality, etc. Or better said, this implies that you get everything, except that your civ knows the brain better than us, better enough to be selective about what they get.
It is not only safer to not be selective but the person going immortal will probably prefer to retain everything. The biological beings that perfected the procedure probably wanted things that way.
The best structure known to store that is an artificial neural network. What is it? Just image a matrix of numbers, representing your neurons weights, and a set mathematical function that rules how a signal propagates through the network and modifies the weights during training, or produces an output.
The beauty of this, is that to learn something new, you don't need to modify the network shape, you just need to expose the network to new stimuli and let the weights adapt.
Different network designs may have different potential, like be able to be connected to different inputs (the senses). To map a human brain those people need to have an advanced understanding of this, superior than the one we have now. Human synapses probably requires a very specific network design.
Now, that's only a simplified approximation. To map a real human weights into a computer there are a series of challenges.
Precision: Can a vector of float/double/1024bits_floating_point_data_type_from_future, represents correctly what we have up there? Or the result is a ugly approximation? At which precision it is cost efficient to backup our synapses in a digital format?
Because you may have all the quantum bits based storage you want, but I can be super mean and fill it with a single BMP (version 4986 from future) file containing a photo of my cat saved with an absurdly high pixel precision, and absurdly high resolution, just to full your storage device.
Artificial neurons aren't neurons: but at the time Andromeda and Milky Way merged people, if still around, probably have some kind of technological solution. Better artificial neurons, maybe besting the biological ones. I can't imagine how biological ones may have evolved by that time. If those people are doing this, then they are beyond any moral war about using our intellect to decide our evolution. So biological ones may be a thing themselves too.
The perfect robots are probably... humans. They can use tools, and come with a very debugged firmware that guarantees a natural predisposition to survival and reproduction. When going digital, are we getting a good deal? Only relevant, of course, if they had a choice.
Why retain individuality? Except that your civ knowledge is complete, and I believe that just can't be, there isn't absolute answers for everything. So you will need to roll a die sooner or later.
And if your civ is with me in this, they like individuality, and that implies different skillsets, and creative ways to use those skills. Two astronauts with the same training may take different decisions given the same situation, and both may be right or wrong at the same time. One may decide to repair the ship, the other has the same skills, but facing the same situation decides to abandon the ship. And both may survive.
Your knowledge VS shared knowledge: our transcended people are past the mechanical layer and can access the Internet faster. But for safety they are still isolated. Their own knowledge (and personality and etc) is the one encoded in their synapses (or virtual emulated synapses), the shared knowledge exists in... HTMLv1024? records in the... Internetv2048? And still need to be accessed and understood. And each individual, digital or not, will understand the records differently.
Of course, digital people can simulate hypothetical situations faster than us. They use faster the same tools (referring to software at least), and they can use some tools made specifically for them, once evolved as digital beings. So standards on everything may be reached faster.
Digital people may decide to abandon individuality. People are different, so some may do that. Will this kind obsolete the other? Not necessarily. They may even be inferior in a lot of ways.
Digital people may be very fragile. Better that your hardware is super robust. Resistant to radiation, lighting and who knows what. They need to be aware that there is a physical universe out there and have efficient tools that they can operate to continue improving and repairing existing hardware.