Ah, not so quick! My fight with this is far from over! Darn, I should have tested it a bit more.
It looks like if I move the UA-based rules into the <Directory>, it no longer applies to URLs created using .htaccess but it I use ANY <Location> based directives, none of the <Files>-based one work anymore. What the heck? Anyone knows what's going on with <Location> directives canceling out the filesystem-based <Files> and <Directory> ?