It can be the same signal chain.
For example:
Single amp block, connected to FX loop out and a cab block. FX loop out goes to a real amp and cab, cab block goes to front PA.
The IR is taken of that real cab.
The Speaker page is set up correctly for that real cab, therefore for the cab IR too.
Speaker compression (or anything else cab related) is off in the Amp block. Cab block has motor drive dialled in to compensate. Even though, this is not ideal and I wish you wouldn't have to do that, it's not that bad. This is the old way of doing it and it worked great for everyone until it became an amp block thing.
if you like the tone from the real cab, but not the PA, compensate with an EQ block, or the global EQ controls.
Headphone out, well...
You don't ever listen to a PA, the headphones and a cab on the same time.
If you made your preset well, it should sound the best it can sound through whatever...
I really don't get the idea that you need a separate setup through your monitor headphones and your monitors....
But If you just want to jam though your headphones and you for some weird reason dislike your normal guitar tone through your headphones, make a separate preset for it.