IMHO from what's been posted, it looks like Deactivate shouldn't be there. NoMerge is fine, because otherwise the plugin might get merged, in which case it could be deactivated, leading again to the problem of the BSA not loading.
I don't think renaming the BSA is appropriate, since that's obviously not how the mod's supposed to work. It looks like the Deactivate tag needs to be removed.
As for the mod overwriting the changes of other mods, that's why those other mods should be tagged with Import Stats. Unless I'm missing something...
Though I do think that it's bad design for something that purely replaces graphics to be dependent on a plugin loading a BSA. That's the sort of case where loose files are more appropriate, so changes can be imported and a plugin slot freed.
Oops, this is my fault. I became active again recently on the BOSS project, and I've been doing a run of tagging some pure graphics replacers with Deactivate, which reminds people not to check them. However in my setup I had extracted the BSA to a BAIN package precisely to free up the esp slot, and so the Deactivate tag worked fine. Yeah, packaging replacers in a BSA is a bad idea. So, after reading your comments I removed the Deactivate tag but left NoMerge (at least one of the Alluring Potion Bottles.esp was mergeable).
Edit: from what I read in one of the past MMM threads, the modified date of a BSA and other factors can affect whether resources inside it succeed in actually replacing vanilla resources. It would be worth a note for that mod in the masterlist, if someone can come up with 100% reliable info on this. Apparently OBMM changes the date of BSAs when extracting them from archives while BAIN doesn't, which further complicates the issue.
While we are on the topic, are there any objections to my adding NoMerge and Deactivate to http://tesnexus.com/downloads/file.php?id=13012 and LoadingScreensSI.esp? Currently LoadingScreens.esp is only tagged with graphics and is mergeable, so Wrye Bash will propose to merge it. Bad idea, it could overwrite another mod such as the ones that add loading screen quotes. There's absolutely no reason to activate or merge these two plugins as long as you import the graphics, so the additional tags makes perfect sense IMO. Just checkin that I haven't overlooked anything.