One tip for merging and using BOSS is to either use Surazal's BOMM or just rename the final product after a mod recognized by BOSS (I call that mod tucking) so that it will be sorted. Then by following good bain packaging have the merge bain package load later and overwrite the original esp.
Generally for fancy merges though I create a bain package with all the replacers combined in with the merge result esp for good measure.
You'd be surprised though merging more and more mods can have a similar result of having more and more mods except with greater levels of complexity - I've had mergers work great at first then down the line damn if that wasn't the issue that makes the game crash every 2 minutes. the more you add the more chance for conflict-testing-frustration that whole cycle.