View Wrye bash as this...2 sides of a fence.
Skyrim Folder | Skyrim Mods Folder
On the <<left is the game folder IE data/textures | >>Right side is your Zips & or Projects in the Bash installer directory.
That out of the way, a mismatch is nothing more then Wrye bash seeing a difference from one side to the other. could be anything, you edit an INI (in the game folder),and you now have a mismatch, you change selections in a installer , mismatch. You delete a file..Mismatch it all depends on what the mismatch is. ( I did a video showing how to create a BAIN installer then touched a little of this in the video, waiting on Youtube to verify me...lol).
Conflicts....File conflicts, say one texture from one mod is the same as another mod, what ever mod is loaded first is the Loser, the mod that is loaded last is the winner. no need to remove or delete anything, Wrye bash shows you the conflicts, if you move one mod below another mod it will now be the Winner (this is assuming you have your Wrye sorted by Load order), Wrye will know what to do , it will remove / place files accordingly.
Mod a
Mod b
IF you click on Mod A and look at the conflicts it would say that mod B is higher (Winner!)
If you click on Mod B and look at the conflicts it would say that Mod a is Lower (loser).
Sort all tabs in Wrye by Load order. Then from top of page is start, bottom of page is finish, as we load files they get overwritten by the next mod loaded.
Boy that was hard to make clear. :)
The question it's self was hard to make clear also. Your explanation was very good. So much thought, for something so unimportant. 
Answered
