I will throw in my thoughts too.
There should not be any hard version lock down, so just a warning message but no refusing to work.
There should be a separate version for the game content and the Engine/API since modding is a big part of the game since the game itself is a mod.
Regarding splitting version between the game and the engine, well you can not really compare it to Minecraft directly since Minecraft is one "blob" with the game engine and game in one, but if you really want to compare it, in modded minecraft pretty much everyone uses forge which has it's own version, so yes there are 2 big versions in modded Minecraft too.
There should not be any breaking changes at the 4th level. 3rd level maybe if it is just a tiny thing that might break something but probably wont, 2nd larger changes but still not huge changes. 1st level huge changes like changing the world gen completely.
(A bit unrelated but copy mentioned it) I am totally for having a mod repository but there should still be easy to just add a zip/folder/c# file directly to the game.