if you use some tools that actually modify the original game file, you can end up with some issue at some point. The most common, will be the need to download the whole given archive file on game update, instead of the updated data. However, you can use mods that produce (or come) as "loose files" or extra archives (ba2) without cumbersome actions nor any risk of file corruption. If Bethesda choose to not allow those at this end, they will invalidate the overrides mechanism, (which is actually availible by default in the prefs.ini files) and nothing wrong happen to your installation.