Archive Invalidation does not work that way. Loose files will ALWAYS have priority over archived files, ESPs are not a factor.
The ESPs are dummy files, they contain no data. This is one of the ways to tell the game to load a particular BSA Archive (by loading an ESP that is named identically to the BSA). This does not interfere with loose files having precedence over archives.
LOL, I have a misconception from 10 years ago (since MW) until today about the .esp files, the loose files and their precedence ...
Excuse my previous paranoia...

So I can have the best of the 2 worlds: HD textures 2048x2048 from 3
rd party
AND HD textures (supposedly 1024x1024) from Bethesda for everything else that the mods do not change ... NICE !!!
