Is Vortex capable of detecting mod-BSA-packed files that may conflict with loose files and/or other mod-BSA-packed files? As far as I can tell, the answer is "no" because I never get a conflict alert (or resolution pane) on loose files that I know are in conflict with BSA-packed files.
Since loose files always override archive-packed files by default, it would be nice to have Vortex parse mod archives so that we could say "No, use the mod Archive's file ('Load After the loose file')" in this case," same as we can when loose files override other loose files. Of course, since the very purpose of most mods is to override vanilla game assets, I would not think that Official Game BSAs would need to be included by default, although a toggled ability to include them would be great for certain troubleshooting efforts.
I believe that MO2 includes this functionality, but that belief is based solely on reading about MO2- other than two tests ending in a decision that it wasn't worth the trouble born of its complexity, I have never actually managed a load order with it.