A question that will garner more interesting replies if asked on the Oblivion forum.
I'm assuming you would want to do this for the compression a BSA provides.
As it is the game works like this - files from the main game BSAs load first then BSAs from other mods then the loose files.
Problems could arise when using replacers - not just texture replacers, but say a mod that does many things but also replaces a texture or mesh from the main BSA files.
Loose files will always load last and that is the way it supposed to work, but there is inconsistent reports as to how well two BSAs with the same file name manage which file gets loaded. I'd heard reports of it being a coin toss as to which one gets loaded even if one BSA and the esp it is associated with has differing timestamps.
There are many (myself included) who have taken texture BSAs and repackaged them with favorite replacers, but there is a maximum limit to the size of BSA files - some details http://www.gamesas.com/index.php?/topic/881204-the-oblivion-performance-project-topp/. Not sure if it is the same for F3.
With Oblivion there is also the issue of http://www.gamesas.com/index.php?/topic/941296-bugz-oblivionexe-filedirectory-thrashing/ - the basic idea being that there is a maximum number of esm/esp/bsa files before the engine starts throwing errors. For Oblivion it is somewhere around 320-380 (varying reports). Again not sure if this is true for F3 too.