The absolute Sprite box size only sort of matters. The sprite you use doesn't need to be rendered at all so that really doesn't matter. The thing that matters the most is going to be unit count and if you already are having trouble. As a matter of fact, I usually always use a number of collision sprites for overlap tests and never render them at all, but it can bog down with many units. If you are testing overlaps, construct has a decent algorithm for narrowing down the number of items it has to test. Obviously, the more items in collision, are then more items to test range against. But in no way is construct events going to be able to outperform behaviors. Likewise those will never beat unity or unreal.
This is a tough problem, and kudos for trying to build an RTS in c3. Unfortunately, if you are trying to build a massive RTS (on the scope of say COH, SC2, Supreme Commander), you probably can't. Not unless you are willing to compromise massively, build your own pluggins and behaviors, etc...
I advise you run alot of tests. Figure out what you NEED, and then determine how many units you WANT. Create some tests.
If you want 100 units per team and envision 4 teams possible to be built, then a simple 400 unit test map can be helpful.