Thanks for your quick and kind answer. For now I'm afraid I'm leaving MO behind, Oblivion current modding scene doesn't seem that adapted to it yet and I'm pretty much a "newbie".
Well, I think the title of the post is self-explanatory. Is Mod Organizer able to work around the .BSAs issue? https://www.neogaf.com/forum/showthread.php?t=405321