Ahhh... what a pain. Now Merge Plug-ins won't even work for a lot of these files. Since the ESLs seem to kick up USSEP above Dawnguard, Hearthfires, Dragonborn for some odd reason (even though that isn't the case in the Load Order). So when trying to merge anything that references USSEP, I'm screwed. Like I want to merge all of the Farmhouse Chimney's patches for Arthmoor's mods..which also calls on Cutting Floor and USSEP. But Merge Plugins shoots out errors that USSEP is coming before the official DLCs and can't proceed. This is happening with Morrowloot patches as well, and others. It seems nothing wants to adjust to ESL and creating oddities. :( After all of this time, Bethesda gave us a great thing.. and now I can't use it right. Ugh.
Again, not criticicing your app.. Just gotta get it off my chest.