I run mostly FF dev & nightly and I've had it happen to me multiple times. I'm assuming the Pocket getting re-enabled problem is the result of an internal update to the extension that caused it to re-populate all the defaults in the config.
The other config settings I'm going to be less charitable about considering there would be no rational reason for an update to ever change those values.
I've never had the other settings change values either, I suspect you either ran into some bug or the sharing of a profile between dev&nightly is blowing this up.
Maybe - but definitely no sharing of profiles between dev & nightly and as you can see based on other comments in this thread I'm not the only one that has witnessed the behavior.
The other config settings I'm going to be less charitable about considering there would be no rational reason for an update to ever change those values.