No. Subfolders are currently a can of worms to me. Shall I scour subfolders looking for custom .2da files as well? What if I find more than one with the same name? Can I be sure that I am finding the same one that Obsidian is detecting?
I don't think it is too much to ask players to simply move .uti and .2da files into their Override root folder, perform KSE edits, and then move back. Otherwise I'm just setting myself up for bug reports that I'm innocent of.