First, this is a question and not a game killer in any fashion - everything is working mostly as I expect, and I'm just truly curious about this.
As per my usual process, I sort mods via LOOT before I create my bashed patch. I create the patch, no problems, no issues, all is working. What I find interesting, and what I'm curious about, is that when I return to MO, all the plugins deactivated by WB to create the bashed patch have been moved in the load order to the end, after everything that's active.
I don't recall this happening when I was running through the original MO. I've been re-sorting via LOOT afterwards as a 'just in case' measure, but it doesn't really appear to be hurting anything... but I am curious if this is intended or not. Or maybe I just completely missed something somehow?