I don't see any problem with sealing under the removeable parts, since they are all off during the stain & finish process anyway. I always seal the barrel channel and the end grain under the buttplate. You might have to scrape the inlets a little to get some of the parts back in again though. No biggy. Sealer coat soaks in, so no problem, but finish will build up.
Agreed, originals show no finish under inlays, and that is why so many brass parts are sticking up out of the wood years later. IMHO.
I NEVER even THOUGHT of sealing the rr hole!