I think you have mix of good/workable ideas but they unfortunately clash with other concepts that are already in the game. Both Penals and Conscripts vanilla look like they could work. It's everything else around the game that make them fail.
1- All factions are able to build a complementary unit to their starter one from the get go. Moving Conscripts to T2 is weird. Either case of applying the experimental change or not, you end up with one tier having 4 units and the other 3.
I see no problem with that. Each faction is different and there are no rules.
Worse case scenario one can simply move Zis to HQ available after T1 or T2 is fully teched.
2- Penals had always been elite/semi lite units and it might be weird moving them to be Osttruppen like units.
If they are "elite/semi elite" they are timing is wrong. It is as simple as that.
Not sure if they are too good (Osttruppen like) or too bad because they don't have access to a strong support unit like the MG42 nor a transition to a strong unit like PG/LVs. We haven't seen too many Osttruppen games on the preview patch so not sure how successful that design can be. On top of that you didn't suggest anything to make them be good late game.
Osttruppen are defensive infatry, suggest Penal are offensive so there is little analogy.
3- Penals are designed to be good on their own while Conscripts are modular based on increased amount of tools available through commanders.
Conscripts with 7 men upgrade are fine with or without commanders.
4- I'm on the boat that 2x PTRS design only work when they are also good as AI. You need a completely different profile and increased number of them to make them equivalent to other factions AT infantry units.
Not really other AT infatry far more expensive. The idea that PTRS units should operate on their own vs both infatry and vehicles is flawed to begin with and a recipe for trouble.