The US has something called the Unified Combat Command. Essentially what it does is act as a central command structure to bring in multiple different branches in a theater so that an operational objective can be achieved while emphasizing and flexing combined armed operations on a macro scale.
That said, the US military still has branches and soldiers typically train, wear attire and take orders from their branch. Orders and the chain of command will typically percolate through a single branch. So, for example an army officer isn't going to typically order a pilot to sortie. Rather they might contact a controller in the air force who would pass that information to say an air force colonel or whoever is handling operations on a base. Culturally speaking, soldiers identify more with their branch than their overall unified command. Their uniforms, virtues, beliefs and etc all revolve around the branch.
However, why would a modern/near future military on a planet (no interstellar/space) chose to base the command structure around a command zone? Putting more importance on the regional/overall command than the branch itself. In this regard the branches would serve to train personnel at a baseline and manage the logistics of defense procurement/ overall logistics, sending newly admitted/trained soldiers to different command zones etc. Essentially a lot more administration work. Soldiers would receive their higher-level training at command zones rather than with a branch. They would wear uniforms associated with their command zone rather than a branch uniform (of course they would still don a pin or patch indicating overall branch but not as much as the command zone). Ranks would be awarded through a command zone rather than a branch (all zones have to have the same rank structure). Culturally soldiers would identify more with a zone rather than their branches etc. The delineation between bases wouldn't be around the branch. Rather its purpose. Like an airfield would be an airbase with multiple branches on it by design rather than an air force base that happens to have some other branches on base from time to time.
A few reasons that I came up with is that maybe the military favors decentralization after a certain point. Or that the technological/military equipment overlap is so great that mission/equipment specific training isn't so feasible for any given branch (the F35 for example is shared by many branches. A similar thing can be applied for drones). Another is that communications aren't guaranteed or due to the highly mobile nature of war in both macro and micro maneuvers, waiting for a branch to green light a move or offensive would take too long. However, I am not terrible happy with these reasons and am still looking for a more concrete reason why.
Some context to help:
The entire planet in this setting isn't unified or navigable like on Earth. Significant pollution and other plot points mean that some parts of the planet are inaccessible. So there are a lot of dead zones. Humanity also doesn't have full ownership of the safe land either. Some areas are yet to be reclaimed as certain parts of the planet become more habitable.
There are nations across seas, continents, landmasses etc.
Communication methods aren't always guaranteed, especially over longer distances or as a function of time. Part of it is due to intense and major breakthroughs electronic warfare, another part is that the environment can be intrinsically hostile to radio, light, long range acoustic etc communication.
There is no weaponization of space or space-based activities. For plot reasons, there's no satellites and humanity doesn't have a practical way to reach the stars (outside influence). At best there are high altitude balloons for something to mirror satellites or to ping and jump any signal that it catches.
There is a heavier emphasis placed on vehicular/machine combat. The environment is actively hostile enough, but the weapons are very nasty. Proliferation of drones, smart munitions etc means that infantry in the open is a good target. Thus all infantry are mechanized into IFV/AFVs. There is layered active protection systems all over the place, from on tanks to IFVs, to air crafts, to even the squad level where a robot or counter air drone can intercept warheads. Infantry doctrinally speaking for this nation don't operate far from their vehicles unless for a special reason such as environment or special missions.
The nation state in question doesn't have the same industrial capability as other nations. While its not a small army by any means, the military tends to emphasize skill/accuracy/quality greatly. This is rippled through in design considerations such as ammunition and weapons. Instead of using suppressing fire like we do on Earth which emphasizes rate of fire, they use a heavier caliber w/ a lower fire rate to get accurate but sustained fire on a target. Military education on all levels is emphasized as a result, so resources aren't wasted and so that soldiers have a better understanding of what they have to fight with and how they need to use it to beat an opponent that might be their peer or better.
Enemy combatants are all fielding combined arms assets. Rarely will a front or theater feature only army units or a specific type of equipment (such as mainly tanks w/ little air cover, or a lot of air cover with little tanks). Enemy forces can bring a range of weapons, doctrines and equipment quickly. But their employment and overall doctrines are different from each other.
Guerilla warfare is infeasible as other nations have little to no qualms about deporting or killing off an entire occupied territory should people resist instead of assimilate. This is the norm across the entire planet.
The military force is primarily concerned w/ defense of territories over offensive actions unless an invasion of surrounding territories is planned. At that point branches will pull equipment from different command zones and redirect it to other areas if need be.