This is also a problem for me, so good to hear that it could be addressed.
Is there a way to use a more user friendly folder on Android? I am having trouble with enumerators not being able to find the right place - even before multiple project support (which is great by the way!)
Can ODK Collect access more generic spaces on a device e.g. ODK/layers
I know there are technical reasons for having migrated away from a main ODK folder for instances (not sure I really understand them!), butt drilling down to Android/data/org.odk.collect.android/files/ is more difficult than my folk using ODK Collect are comfortable with.
Personally having multiple places for the mbtiles file to reside would not be great (it sounds like you plan to have a general folder and project specific folder) - because I know that if it can go wrong, it will. And the non-human-readable format of the project names on the device complicates things further (as highlighted by @Florian_May above)... Finding yourself out in the field in the wrong project space needing to move mbtiles on the device is stressful enough, but getting someone to do that while they are on the phone to you asking why they can't see the map (when they've finally got signal) is a nightmare. Speaking from experience!
The other useful thing would be the possibility of downloading mbtiles directly from a Central server (maybe this is a different feature request) - if there were a function to upload mbtile as 'media' with a form definition, and for ODK Collect to download and transfer that to the appropriate folder, that would be a great step forward too. And would solve my hassles above...
Many thanks for your ongoing support and development.