The implication is that they will - everything seems to be "once you create a system, normal BGS rules apply", and every faction is only native to one system each. Of course, a retreat could only happen if at least three other factions also got into the system, which probably is sufficient to stop most oddities.
Main problem I suspect is the system having only 1 faction (The faction that creates the new system, in a way) and it's just immediately at 100% influence, triggering expansions that cannot be stopped until another faction expands in, and essentially locking out that faction from normal BGS activities in the bubble.
I wonder if when the system spawns as a proper BGS system, it'll have the faction that created it as a non-native alone with no other factions, or if it'll have it as a native faction, or if it'll spawn in a few proc-genned native NPC factions. Systems don't really need to have native factions, as shown by plenty of systems like that in the bubble.