You've answered your own question there.
That's why I did not strongly argued to simply remove the penalties, but "look into it".
Buffed UKF tanks are great, but costs extra amount of fuel+mp designated for the commander tank. And addition to extreamly high pop for UKF tanks, it is very hard to designate one(even chromwell). So in almost all cases, you end up with AEC if it survived during the mid-game.
If you think about 1v1 there is not really a huge amounts of tanks at the battle field even in late-games. (Top-most 3~4 middle), loosing one simply to buff other is very harsh penalties. So I'm suggesting to reduce the buff & penalties a bit so it can be widely used even with 1~3 tanks.
P.S.
https://gfycat.com/ko/hairymelodicblackfly this gif is probably the good one to back me up on how commander upgraded tank is useless in dealing dmg.