Yeah there is no "plugins enabler" required, that's just a starfield thing.
If something is overwriting your plugins.txt it probably isn't Skyrim. Maybe you're launching something other than the actual game? Such as a mod organizer type of thing which isn't working correctly. Skyrim itself definitely should not do that, nor should skse64_loader.exe which is what you'd want to run instead if you have skse (a very widely-used mod).