For a hour or so I've tested a few things with both Skyrim launcher and Wrye Bash just to see if there were a way to let Wrye Bash detect only active mods in the leveled lists while rebuilding the bashed patch.
My conclusion is that only plugins.txt in the C:\<User>\<Username>\AppData\Local\Skyrim folder I mention here can and will detect any active mod that's properly added in the leveled lists in Wrye Bash, but I also found that the only way to let a deactivated mod to be excluded in the leveled lists is to hide it.
So if you hide a mod then the Skyrim launcher will detect it as such a mod that isn't active, but ghosting a mod in Wrye Bash aren't sufficient you must hide it otherwise the Skyrim launcher will still detect it.
I also check the ghosting a mod feature there is in Wrye Bash and despite a mod is ghosted the mod it self will be detected in the leveled lists, so I think the ghosting a mod feature as it's today can be disable or even removed from the code of Wrye Bash because it won't work properly with a detected mod in the leveled lists.
To summarize it... What purposes has the ghosting a mod feature in Wrye Bash for Skyrim, if a mod are still detected as an active mod in the leveled lists?