No: *all* user presets should be stored in a user-writeable location: that ~/.lv2/
The ~/ is *always* the current users home directory. The "." before lv2 makes it a hidden (by default) folder, and lv2 is the name. Hence, ~/.lv2/ is a good place to store user-presets, since the user will always be allowed to read/write presets to there.
If lv2ls / lv2info are throwing errors about invalid .ttl files, then there's some plugins / presets messed up in your .lv2 folder. The exact errors will have filenames in them: remove those plugins (by deleting the files).
Support for this type of thing is faster on IRC, i don't know do you use IRC? The following link will allow you to talk in the #lad (linux-audio-developers) chatroom. Explain the issue with .ttl files, and somebody will help you, or I will if I'm online
I'll give IRC a try, I haven't needed it yet, but it's probably the right time. Thanks! I'll try it (hopefully) in a few hours.
I'll check the exact output for the errors and see to cleaning that up..