What irks me a little about it is the fact that it's just so arbitrary and a bit of a kick in the immersion too; no doubt they are locked to allow release of some content at some point which in itself is good but there's no canonical reason why it's happened (or indeed how it's happened - who can permit lock entire sections of the galaxy?) Reminds me of when Dorothy looks behind the curtain.
My headcanon for permit locking is that there exists technology capable of emitting a signal that prevents your FSD from obtaining a positive lock on the star(s) in that system. I.e., if you can somehow "scatter" whatever reading the FSD/ship sensors use to detect the star mass, then your FSD won't be able to guarantee it can drop you into the system properly, so it won't jump. Having a "permit" means you have the key that decrypts this signal, circumventing the scattering effect.
Theoretically this could represent the emergence of aliens. It's also possible that there is a human presence at work: perhaps a faction has journeyed out here and tried to stake out this territory for reasons as-yet unannounced. Maybe it's to do with the Dangerous Games, with the meta-alloy storyline, or with the ongoing Imperial/Federation brinkmanship.
Would be nice to see some Galnet articles (maybe player-submitted) about "stranded travellers" finding themselves having to make huge detours now that entire sectors are suddenly inaccessible. I think
that would help with the immersion aspect.