> I've worked with design systems which have a <my-layout> component near the root which defines sidebar, header etc slots.

Funnily enough this is exactly what original proposal of web components was against :)

Honestly I couldn't care less what the original proposal said! Things evolve. Utility is found in unforeseen places. That's the nature of ~everything. Personally I'm not a fan of that kind of component but not aligning with some original, preordained vision is a minor nit