If Illgames was in any way trying to prevent modding, they're doing a piss poor job.
In accordance with Hanlon's razor, I'm more inclined to believe it's just the lead dev flipping the Editor switch from JIT compilation to AOT compilation, with the (correct) belief it would increase game performance.
Modding loss is a side effect of losing easy access to IL/.NET types and having to deal with ASM instead - since the game is, you know, actually compiled to ASM this time - but I don't think it was the purpose of the change. If they were actively trying, they'd have toggled the next checkbox, which is code obfuscation.
Doesn't seem to stop ManlyMarco/aldelaro5, frankly.