That is one of the points of squadrons, align to power, superpower and faction.
My confusion - from lack of knowledge in this area - means where do these cross over. eg: Under what circumstance if you align to X does that mean you're also automatically aligned to Y.
eg:-
Aligning to a Power means you're automatically aligned to a Faction (eg: Federation)?
Aligning to a Minor Faction might mean you're aligned to a Faction?
So with my suggestion that when a Squadron is created, its Power, Faction and/or Minor Faction are defined, would simply mean those need to be sanity checked. eg: If you assign your Squadron to be Powerplay "Arissa Lavigny-Duval" aligned, that means your Faction would automatically be assigned to "Empire" too etc.
Thus, if someone joined that squadron, they would not be allowed to join any other Powerplay or Faction or Minor Faction role Squadron. But they could join say upto four other exploration, mining, xeno ones etc...
We therefore now have CMDRs able to join multiple Squadrons with a sensible level of prevention of split loyalties.
AND, I'd even suggest when CMDRs are switch to that (Duval) Powerplay Squadron above they are automatically pledged to "Arissa Lavigny-Duval". I'd even suggest then, when switched to their other Squadrons (eg: their Xeno or mining ones), their Powerplay pledge is set to none?