Yeah since I can't sop using Bash - this maybe part of what is messing me up.
Really the need is for Wrye Bash to be able to either handle multiple installs or be able to have multiple Wrye Bashes that are separate from each other.
This is a large step in moving toward managing multiple installs though.
I made a crude utility that allows me to switch between multiple copies of TES4.
It handles switching the Profile.txt and DLCList.txt in the Application Data folder, switching entire profile folders (including savegames and the ini) in My Documents and swapping the entire game folder.
It also swaps your bash mods folders for you to.
So anytime you switch you are working with an entirely new app environment.
Caveat is that you have to keep a copy of your tools installed for every copy of oblivion you have.
Also you can't install wrye bash in an external folder.
As long as wrye bash, obse and whatever tools you use are installed locally to the game folder, all of their settings will be retained.
This works great for me. I can still use wrye bash, it detects the correct plugins and I still still have multiple save profiles for each app instance.
You could make a batch script that does the same.
The only benefit of my util really is that it takes care of creating new clone copies and tracks which clone is active.
I could fix it up for public release though if this is something people need.