Do you have a source for that claim? Mozilla's 2010 justification for dropping WebSQL was that SQLite doesn't implement a particular standard of SQL (incidentally no SQL implementation does, SQL is notorious for that, every vendor implements something slightly different with parts of the various standards excluded and other features included.)

But more to the point, Mozilla's gripe was with SQLite's API, not with the file format used by SQLite. I can't find any source for the file format used by SQLite being the problem that tripped up WebSQL.