That being said, I think that such an abstracted system might indeed help with some issues.
E.g. you could erlate some factors in the RTS to the number of invading "unified troops":
A larger army would give more starting units, probably more recruits or even increase income or reduce build times/cost.
On the other hand, moving individual and distinct units (or rather squads) has some merit to it, as well. In RTS it is a difference whether you attacked with a bunch of fast hunters or some slow warlocks, as an example. Attacking with a well-composed army might even secure an outright victory against a weaker enemy, if you manage to rush him before he gets his defenses up.
I tried to solve this problem in my latest comment above. In my system you would be able to "buy" units at the start of the RTS battle according to the number of "strategy map simple units" you sent to battle. So the strategy would shift but it would still be there, especially if you want to engage in RTS mode.
But if not, you wouldn't have to rely on a system which is directly "ripped off" the RTS mode and transplanted into strategy mode without ever really fitting. The rules on the campaign map would be different to the ones in RTS (which is also true now but with - which is weird - exactly the same units as in RTS) and there would be a clear difference between the modes with a better chance to create a reasonable transtion...
