It wouldn't take a convoluted SOP to decouple ALT or V/S, change the pressure setting and then recouple.
No it wouldn’t! I’ve operated on mixed QFE/QNH ops for years. Nearly all sub-scale changes are combined with a change of alt/ht/FL, so if the AFCS is doing the work the only potential gotcha is in a Bombardier-type AFCS where you have to initiate the descent (or climb) in VS or FLC, then change the sub-scale. Certainly in the Global, if in ALT, the AFCS would follow a changed sub-scale - it became second nature to move the Alt Sel, initiate the descent, then change sub-scale.
Waddo RNP T&G to join necessitates a change to QFE in the upwind turn, you then level downwind at 1000ft QFE - simple!
Few occasions one may stay ‘level’ is perhaps on a handover between MATZs: “Set Conningsby QFE, adjust to 2500ft”