The basic problem is that single-faction control of every asset in a system doesn't work as well (BGS scorekeeping aside) as the assets being split between factions. So it makes sense to split them up as a the default, because it's not like most BGS-neutral architects are going to think to specifically spread them out, and let the minority who really want a single-control system arrange that through the BGS.
Similarly when they added all the Odyssey surface bases back in 2021, they didn't just give all of them to the existing controlling faction of the system.
(With how susceptible newly colonised systems appear to be to going to Lockdown at the slightest provocation, spreading out the assets is just safer, too.)