I think your frustrations are partly due to not completely understanding the Lazarus architecture. I haven't worked with Android, so no opinion about that part.
Delphi "oozes" into the registry to store its settings.
Lazarus, being cross platform, does not use the registry and uses a directory (the "primary config path"/directory). It correctly uses the OS specified directory for this (e.g. somewhere under c:\users\... for Windows Vista+).
This arrangement allows seamless side by side installation of multiple Lazarus instances that don't interfere with each other at all - as long as you use separated config dirs and start Laz with the right --primary-config-path parameter to point to this dir.
E.g. fpcup uses this to create entirely self-contained FPC+Laz instances - no need to even mess with the PATH.
Good luck - reading about Android development on the forum and wiki, it seems the amount and variability of the components does lead to a lot of complexity..