Detouring can be done for already detoured functions. Just look at Steam Overlay vs other systems that hook into Direct3D, they can coexist.
I've made my own hooking library that lets multiple plug-ins hook the same function, but it only works decently because it has this central library synchronizing access.
Naive implementation of this scheme doesn't allow stacking.
Meanwhile, the Microsoft Detours library supports detouring other kinds of instructions at the beginning of a function. It's not exclusively for the 'two byte nop and blank space' thing.
2) Thread A reads original instructions while thread B is replacing them, such that it reads part of an original instruction and part of a replaced instruction. Thread A’s trampoline would have nonsensical instructions.
There is a setting to make it pick up overlays, which works reasonably well, I'm not entirely sure how it's implemented.
Then you're faced with the problem of how deep your hook is, you either want it to run early (before other hooks), or late (after other hooks but before actual function). When you're trying to capture the overlay, you want your hook to run late.
The cop-out is to hook D3DKMTPresent instead and hope nobody else hooked it.