(Disclaimer: I'm mainly running self builds of trunk on Linux -- no install -- but *with* different sets of AddOns managed by my own oolite-wrapper. Also my exposure to the ManagedAddOns is zero because I'm always manually managing my AddOns -- you may call it a Slackware old habit).
This doesn't seem to have any effect on the location of the AddOns or the ManagedAddOns folders (both of which remain located under the default ~/GNUstep/Applications/Oolite folder).
The safest AddOns location to mess with should be ~/.Oolite/AddOns. I'm actually soft linking it to my Windows various AddOns folders (for visuals, some shader studies, Random Hits)
I'm getting the feeling I'm going about this the wrong way. What I'm after is one instance of Oolite that includes the various OXZs that I have selected for normal play, and a second instance of Oolite that only includes OXZs that are currently under development or testing.
You can always prepare your own sets of AddOns/ManagedAddOns folders (e.g. AddOns.Normal/ManagedAddOns.Normal, AddOns.Dev/ManagedAddOns.Dev) located at your convenience in the filesystem, and link them to the desired location in your wrapper script during startup (oh, and yada-yada, either Shift start or do the same with the cache and any other GNUstep configuration files you might want adapted).
Hope this helps.