So I tried repacking my mod with the proper filenames, and found that it worked that way too. Able to start with just the ESP+BSA and the loose file shuttled off to a folder outside of Steam.
Can anyone else confirm this using 1.4.27? I am suspecting a possible stealth fix in the game's beta patch since I know this failed under the 1.4.21 official version. If so, Bethesda's team really needs to work on change documentation because we like to know about fixes like this

