At the risk of entering the global "stock vs. mods" debate, let me express my $0.02 concerning new patches and compatibility of mods.
Let's first separate mods into two categories:
Category 1 touches base game files, be it java classes, 3d meshes, effects, maps, hell even simple properties or ini files.
Those mods cannot and will not ever be cross-compatible among different base game versions, for the simple fact that what those patches modified, most likely is getting modified again by the next patch released.
We cannot blame TD for this.
Many times we cannot blame the modders who made those mods either, because many of the enhanced features shown in recent mods aren't possible without touching base game content.
Sometimes however mods don't seem to care much for compatibility issues and simply change files across the whole game, yes it even seems random from time to time, and that would better be avoided.
As a rule of thumb, whenever you create a new mod, try to make it as less intrusive and as much cross-version compatible as possible, hence try to touch no base game file at all and if that cannot be achieved, try to touch as few of them as possible and last but not least, document the changes applied.
Category 2 already successfully followed the recommendation from the last sentence above and doesn't touch any base game files at all, or just very few unimportant ones that don't change since IL-2 1946 aka 4.07 release.
These mods ship full-featured with no cross-dependencies to other mods or specific file versions.
Basically one would expect such mods to work fine when a new official patch is released, but unfortunately most of the times that's not the case, e.g. easily 3/4 existing working 4.12.2 mods will not work on 4.13.
Why?
Because TD doesn't care for cross-version compatibility either.
That's the single most important point when TD would want to reach out their hand to the modding community: Take care of backward compatibility.
It's okay if you bring new content and features to the game.
Just leave the existing ones in place too so that existing mods continue to work on the new patch level (even if they do so without supporting the new features then, this can be dealt with on later mod updates if desired).
For instance this means that instead of altering the functionality of existing java methods, as soon as compatibility issues arise, implement the new functionality in a new method (which can even have the same name if arguments differ). Too much work changing all the method calls in code? C'mon, contemporary IDEs do this for you with one click, "refactoring" is the key to success.
If this would eventually become common sense, life for both modders and TD developers could be much easier.
Unfortunately up to now TD follows the "our patch, our game, we're the state" and gives a damn for backward compatibility.
The longer it stays like that, the more modders will throw the towel and the faster IL-2 will die, this might sound harsh but it's really as easy as this.
Maybe this will change one day, maybe it won't, time will tell.
Best regards - Mike