As to focusing, you can remove/replace spacers (between sensor holder and mirror box), so auto focus can work as before (I think they are ~0.3mm thick, just right to compensate for missing filters).
With camera like this (Full-Spectrum Modified, FSM) you can do NB without problems.
I have UV-IR cut filter in the light path (as drop in), L-Pro is
inserted in the adapter.
I am guessing NB IR filter can be mounted in similar way.