If I have a 97% chance to win when facing a lone Trooper, I should not have to waste my time actually entering the RTS mode myself just so I don't lose two far more expensive units to those lone troopers.
That is more or less the point of the whole discussion: Where is the guarantee that a single trooper does LESS damage to your troops when you enter the RTS mode? Remember, that it is not the lone trooper which is waiting for you on the RTS map, but that your enemy can produce hordes of units during RTS, build bases, turrets etc. I always tend to loose the same amount of units (or even more) during RTS compared to the autoresolve result. And I think that an
average player would do the same. If you recognise that you loose less units during RTS than autoresolve would suggest - then you are probably a very skilled player and undoubtedly
better than average. In that case you are superior to autoresolve and should just choose whether to employ your skills and loose less units during battle or just accept the autoresolve result which is balanced against an average player.
But I agree, that it is the balance issue - PRIMARILY in directly fighting RTS and just SECONDARILY in autoresolve that allows the lone trooper to do such a huge damage. This is just an inevitable consequence of the possibility to produce units during RTS phase.