M'Benga has compiled a hell of a list of justifications for getting demoted already, and (obviously) none of them have actually got him in trouble just yet. Secretly keeping his daughter in the transporter buffer, carrying super soldier serum about his person at all times, killing a Klingon ambassador... suffice to say he's a bit of a wildcard.
Yeah. There is definitely several stories that could play out here, for both M’Benga and Chapel.
Continuity wise McCoy didn't join the Enterprise until after the first couple of episodes of TOS s1, Mark Piper was the CMO for those so there is definitely a thread they could pick on prior to Kirk taking command of the Enterprise.
For Chapel we know she gets engaged to Roger Korby at some point. Will be interesting to see how they move the character to line up with 'What Are Little Girls Made Of?'