In bug 1776566 to upgrade SQLite this assertion started firing which appears to be the result of SQLite newly canonicalizing the database path(s) and implies that we should probably canonicalize any paths before handing them to SQLite on linux and OS X so that the telemetryVFS can then perform the lookup in the same canonicalized-space. Another option could be to try and rely on
PROFILE/storage presumably having a consistent root, in which case we just need to be able to recognize and strip the canonicalized prefix in addition to a non-canonicalized prefix. One complication we should be aware of is that on Windows the Firefox profile can potentially exist across the roaming profile and local-machine paths, but I don't believe the windows VFS is impacted.
Note that I have not re-familiarized myself with the way the VFS/GetQuotaObject is working here (yet) so the above is hand-waving.