Edit: concerning preferences
Adding such features is also quite easy as you have seen, however I won’t do it until a few weeks. Mainly for the reason that I did not work with point clouds in Blender yet, and need to try it.
Posson / marching cubes / Pivot ball … are amongst the features I will include in the code for sure, as they have a direct use for many people. At this point though, the integration of the scanning tools is not prepared, and there will be a little bit of delay before I start working on them.
Moreover, and you are right to ask, I won’t take in external code contributions until a little bit later. For pull requests, that will be 1-3 months I think. For suggestions like yours, which can be easily integrated, something like two weeks maybe three? I still have to create all the adequate code structures to make it really modular, and I will probably refactor everything just before opening it up. I can’t start doing that now, where would be the fun in it?
I will open the code, as the whole idea behind the project would not make sense otherwise, but I need to set up all the system around it, and talk with a lot of people in order to make sure that I manage to keep that project useful, relevant, “state-of-the-art”, innovative… and don’t just recreate Meshlab in blender by interfacing every script (and if you have looked at the code, I also need to implement better ways)
And concerning preferences, the first behaviour is normal behaviour to me, as you did not save the settings, well, settings won’t be saved!
The second one however is one I already planned to fix. Not for people disabling the addon, but for updates, which force users to reselect the paths…