Are quirks officially counted as disadvantages?

[Langy]

Well for one, because it isn't recommended in the book, it's listed as an optional crutch for GMs who have power dynamic issues.

Re-read the 'Disadvantage Limits' section. It very clearly is recommended that you put a disadvantage limit in place no matter if you're a bad GM or not. Disadvantage limits are optional rules in the same way limiting characters to a point total is an optional rule.