That's the first I've heard of that. So MS will face similar problems in future BC for some titles.Umm, no they really can't ? Custom D3D on Xbox One exposes raw GCN2 ISA much like GNM does on PS4. Aside from maybe a couple of registers, they're largely the same GPU architecture. On consoles they can bypass the entire shader compiler.
Which is really bad practice these days! I hope devs drop that. the efficiency gains aren't worth it in the long run. A game should never break because a workload can be completed faster.As for why games aren't able to take automatic advantage of boost clocks, that's likely down to their reliance on timing specific behaviour on previous hardware.
But that said, that's not a problem for a BC architecture that can clock lower for those titles. MS's abstraction allows them to run XB1 games on a GPU with a completely different CU count, where Sony's apparently does not.