It is confusing that there are 2 CustomPress plugins which I understand are the same, just different by location:
- CustomPress: stand-alone plugin
- bundled: such as with Directory
I know you shouldn't run the stand-alone plugin when using Directory because Directory already includes it and adds it to the main menu etc. I also know that settings won't be lost as they are stored with posts so one can switch between those 2 CustomPress (like when adding or removing Directory).
What bothers me a bit and which I would suggest to look into as it had me doubting for a while (and I have seen those questions in this forum as well) is the WPMU DEV Dashboard's Plugin page which should not offer the CustomPress plugin for installation when it is already present (or whatever other plugin already bundling it such as Directory).
This is a trap just waiting for people to click into.