So you think eventually a CMDR will discover a friendly race in one of the permit-locked systems?
I think that having so many permit-locked spheres of space, so far away from anyone and everyone, requires some kind of Lore explanation. My assumption regarding them goes something like this:
Someone - we don't know who, either a freelance explorer or a government-backed expedition - at some point int he past has discovered clear evidence of something significant - whether it be peaceful aliens, "lost colonies" of humans, or some such - in those sectors. They reported this to the authorities, and "They" (whoever They are) decided that those newly discovered beings needed protection. So they paid Universal Cartographics to apply a permit lock to the entire sector of space around the aliens, preventing casual, unofficial, untrained "explorers" from blundering in and ruining a First Contact situation.
Once They are satisfied that First Contact has been successfully attained, they will unlock the permit (or provide CMDRs with some means by which the permit can be attained), and then those CMDRs will be allowed into those regions of space and engage in peaceful activities (dialogue, trade, technology exchange, whatever) with whoever it is that lives in there.
They presumably also had similar permit-locks placed on Thargoid space (such as around the Cone Nebula) - only the Thargoids have chosen not to remain inside "their" protected bubbles. The Thargoid permit-lock bubbles still remain, only the purpose is now reversed - those bubbles are in place to protect innocent humans from the evil aliens, preventing CMDRs from flying into certain death and/or from causing a Thargoid hyper-reaction by having a Human ship blundering into one of their nests.
[OOC: Of course, we can't see any of these other aliens in-game until FD actually creates the aliens; they presumably have not yet done so. But the permit locks are in place, so that, once they do create the alien planets and space stations, the places where they create them remain Unexplored. Otherwise, someone could rightfully say "I visited those stars last year, and none of those alien planets and space stations were there then!"
I strongly suspect that FD's original intention was to release some friendly aliens for us "Soon", but that this project is now on the back-burner. My evidence: the subforum originally titled "Thargoids and Other Aliens" has been renamed to "Thargoids and Guardians".]