Unable to add custom tables to Zotero database

I am writing an overlay on top of Zotero that adds some configuration settings to the Zotero database. The extension uses Zotero.DB.query() to run the SQL.
All my insert/update statements work fine. However, I have some create table statements that fail because the table sqlite_master is locked.

I have tried setting extensions.zotero.dbLockExclusive to false, but this does not change the behavior. I have also tried restoring the database from a backup copy, and the behavior is not changed.

The database does not seem to be corrupt - it's just that the Zotero's initilization SQL seems to lock the table sqlite_master, which prevents running additional DDL statements.

Any idea how to fix / work around this?
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