but what effect will it have on them in the long term knowing that in time SNA will completely outgun them? i don't think they will simply standby and allow this to happen tbh
It's hard to tell. But I'm assuming that the current deadlock between FGS and PL will ease, and possibly reach some form of agreement on their political differences in a near future. PL doesn't necessary constitute a 'threat' to FGS as they officially fall under the government of Somalia.
Regarding SL, as Somalia becomes more stable and the state-building process move forward, a heavy pressure will be mounted on SL. I don't believe either that SNA will use violence against them, but rather diplomatic means to force them to come back to Xamar. All they have to do is tell IC to deal directly with FGS on matters relating to SL.
Moreover, after AS, FGS/SNA will first try to disarm heavily armed individuals and (clan) militias before they move on to anything else. This in itself will take quite some time.