Well, here you go...
Hm, let me go crazy for a minute....
Perhaps the system could be fairly improved by removing all the different unit types from the stategy maps and make a real "Risk-like" approach? So you only produce troopers or "single units X" instead of the units which are translated from the RTS battles to the strategy map...
Well, first of all since they announced that currently the autoresolved is bugged anyway, we might have to wait for the next patch, or need to accept that some points we discuss might be moot.

E.g. if the unit types afterwards factor into auto-resolve in a rock-paper-scissors kind of way, the composition of your army does play a role and is a strategic decision to make.
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.
Personally I'd keep the current system, but adjust it in some ways.
As you say, there is a certain dychotomy between RTS and campaign map.
It is possible to just ignore it and have fun playing the game, but for me at least a small itching in the back of my head remains.
I feel that in order to reconcile the two parts, the effect of map units on the RTS part should be increased. Since the latest beta, this can be done e.g. by increasing the recruit cost multiplier.
On top of this there might be other things that could be done:
* adjust available recruits or income rate by the size of the invading army - more troops, better support.
* make basic units available all the time, but restrict building of advanced troops (e.g. more than 10 research points) so that you can only build more if you brought them with you while invading.
Of course such changes would also mean that "turning" a battle that starts with the odds against you would be significantly harder.
Then again, I think that you should work on the strategy map to prevent something like this from happening in the first place.