To be honest, Unity is a very inefficient engine with a lot of incompatibilities. Since they are making their own engine, they will have complete control of every aspect, and they will be able to make it the most efficient possible for their massive task at hand. For example, Kerbal Space Program runs on Unity, and it has a solar system that it is constantly tracking. It is in early alpha, however it is still extremely unstable when you build a spaceship of 500 parts or more. If PA used Unity you could expect extremely small battles, and a very non-detailed environment. Another game using Unity is Mech Warrior : Tactics, which is an abominal attempt at smooth gameplay, despite it's turn based nature.
BTW I wouldn't slag on Unity too much. Everyone here is very impressed with it for what it does. It's absolutely the right tool for a lot of types of games. The difference with something like PA is that it's outside the wheelhouse of almost all engines. You'll notice that basically every single RTS uses it's own engine. This is because RTS games really are oddball when compared to most others. For example most RTS games are synchronous because of the amount of stuff happening in the game. Without going into details making an engine be synchronous requires special programming techniques and tools to make work properly. On top of that the sheer number of entities in most RTS games requires a different optimization strategy. Tradeoffs are made to try and get the overhead per entity down as low as possible. A very general engine usually makes the tradeoff in the direction of flexibility, not performance. PA in particular is trying hard to push tech in a unique direction. For this reason we had to chop Unity and build our own engine. I think it's likely that we continue to see more games being made with fewer engines in the future.
engines like unity and unreal are great for putting most of the technical work out of the way, and getting games out the door faster and cheaper. for smaller companies this can be great because the entry cost to making the game is much lower and means games are more accessible, HOWEVER it also means that there can be less variation in what a game can DO, unique mechanics and designs are limited to within the scope of the tech supported by the underlying engine, and because the engine developer has to think of how many use cases could use a feature going into the engine it means often if you are trying to be innovative with gameplay, then it is unlikely the engine developer included tech you would need. which can cause trouble. so custom engines have that strength of being able to do what you need them to do assuming you have the skill. no one else decided what you need in an engine. but as neutrino knows don't try and develop something over general in a roll your own only make the features you need it will really control the possibly exploding cost of a roll your own .
Unity "could" perfectly support PA, but it would never be as fast (performance wise) as using a custom engine, and you will have to work around a lot of things, Unity already gives a lot more freedom in what you can do compared to, say the unreal engine. Even the Unreal engine could do it, but there would be even more stuff to work around.