Your not going to get relic to redo the entire OKW teching system in order to get rid of the Schwer.
A much more reasonable suggestion is just removing it's ability to pen mediums, that's all. It can't even lock down that many points unless you get lucky or put it out in the open (were it will die faster).
There are many options to make it less "This is now OKW's territory unless they dumb". They could do as you said. They could reduce the range to 30 to leave it helpless to tanks. They could make the flak cannon an additional upgrade to the building with an appropriate cost and upgrade time ("appropriate" is a code for "I can't ballpark this anymore"). They could make the building more delicate.
The Schwerer is balanced I think. It can't take out Shermans(If their frontal armour is facing the flak truck), t-34's
It absolutely can. The building will have like 20-25% left before the medium tank must choose to run or die.
...Sherman was using HE shells. With AP sherman would win, but you are suggesting that frontal armor is untouchable for Flak. Well it's not.
Versus T34 it's 8/10 for T34 but with every case, T34 has about 5-15% HP left...
You've seen them actually kill it alone?! Excuse me, I have to pray to RNGesus to favour me more.