Jumping in with the same issues here.
Sync is enabled and configured on windows(0.12.15), ipad(1.0.4), and android(1.0.4). Notes sync, but none of the settings, plugins, themes, etc.
I tried to create a separate settings file for my ipad by copying the functioning original .obsidian directory and renaming. changed to new directory on ipad. ipad app is still showing no plugins or themes available despite all being there in the directory.
Running out of ideas on what to try next.