and yes the oxz do work in either directory, but if you already had an install of Oolite on another distro of linux, then you have to migrate everything somewhere if you want the same setup (basically). and this can also save time when you already have the add on instead of downloading a new copy (bandwidth)
Ah I get you, I think you could even migrate the whole ManagedAddOns directory, I've copy/pasted my AddOns directory successfully from another distro.
if you put the oxz in the add-ons folder instead of the managed add-ons, then the in game downloader and updater will have strange results, like mods being in red even though they are technically installed
I believe this is expected behavior, the manager is just letting you know that the oxz is installed in the AddOns folder instead of ManagedAddOns folder and therefore, as you pointed out, not updatable with the manager.
The add-on errors are straight forward and not cryptic.
I agree, very helpful for development too.