The Golem and Spirecraft Exos should not be separate. Instead, each additional exo source should increase the potency of the overall Exo wave. This is for two reasons:
1. Dual exo waves right at the beginning are a bit too strong for what you get (not even going to go into triple).
2. Later on, the exo waves can split up, which, between Exos and CPAs, could mean that the player is on the defensive more often than necessary. This can be worked around if the player can 'coerce' the exo to come from the same direction, and build a really strong whipping boy.
Interesting. I play with Golem Hard, Botnet Hard, and Spirecraft Hard on all the time. I am facing 3 exos, that may or may not come all at the same time. With your idea, I would be facing a single exo, but one that is now 3x the power, all at once. I am not sure which is better honestly. The former is more split up, but I build a single hard chokepoint, so it all goes to the same place. Rather, as they are not spawned exactly the same time, the full power of it doesn't hit all at once usually. This allows for some rebuild time. With the other way, it would all pretty much it at once. While this does give me more overall time between exos, it means that much more enemy firepower is hitting me at once.
While concentrating the 3 exos into a single source does tend to favor the single chokepoint route rather the spread out defenses, it also means that the AI firepower that is hitting that single location is going to be vastly more powerful, especially if you have all 3 options on. This gives the AI a much larger chance of breaching your single superchoke, and thus more likely to cause serious harm. Especially as, as I understand it, the number of individual captains in the exo, and thus the number of squads in said exo, do not grow larger. Rather, it is the power of the captains themselves, and the units they lead, that grow. Using my own case as an example, while I would be facing only a 3rd of the number of squads, each squad would have 3 times the number of points to use. Suddenly everything in those squads gets bumped up a teir, and the squads get much larger too.
I am uncertain how I feel about this idea. While it gives the AI a more effective weapon to try and end the game, which is a good thing, it doesn't have a lot of those honestly, it also makes that weapon so effective that it becomes overly powerful. Suddenly I go from "My chokepoint can handle these staggard, but rather heavy, strikes from the AI" to "Wlep, its Exo time. Either I break out warheads or I lose."