Yes, I believe that would work great. I mean, it's already shown on stage 1 GPF cars that the GPF doesn't affect performance, if anything some make even more torque than before despite GPF's being on. Similarly for stage 2, the issue is the main catalyst. Replace this with a high-flow one and leave GPF's where they are and we should expect similar to pre-GPF gains there too. And I am sure there would be no MOT issues with such a solution.
But I can see where the difficulty lies with that: To keep costs reasonable, exhaust makers need to modify the stock exhausts / re-use GPFs, rather than throw them away completely. Before, there was only one expensive item and it was the one that needed replacing anyway: The main cat. So it was ok to completely throw it away and create the necessary piping around it.
Now, for MOT compatible solutions, if they throw away the GPF downpipe, they need to put back new dual GPFs which is a cost increase and a waste of money as they could have re-used the exact same stock ones, it's not at the GPF's where the gains are made. But for that to happen, it means they need to take the exhaust off each customer's car, modify it, and then put it back, so it can't be an off-the-shelf product like before (if you want to keep the cost down), it's more complicated.
Also, why would I pay for an exhaust with new GPF's when we know their restriction is minimal, instead of re-using mine. Maybe a custom solution as you described: take exhaust off, replace only main cat, put back, is the best value for money option. Can't think of much else.