This is very common especially in older homes. Often you will find beautifully stained woodwork in the Lr and Dr, but painted in the Br's and Ba. What you want to avoid IMO, would be to have different colors in the same overall space. If the kitchen is separate from the dr for instance, it would not be crazy to have a different stain color in there.

See the link below. We have a mix of stained and painted. Turned our really well. Regarding your other post on costs..... We had an absolutely superior painting crew. I don't know the specific break down but staining was about 20% more than painting, but it took several days longer. The painters masked the entire window and alot of the house. Windows were sprayed once, then a day or so later sprayed again and it was done. For staining, a sealer was wiped on (went surprisingly quick) a day or so later, a coat of stain (once again very quick), a day or so later, another very quick stain coat. A couple of days later, urethane, then a few more days later steel wool. Each coat for the stained windows was really quick. They basically wiped it on with a rag. Since everything was masked, they were sloppy and flew. Hope this helps. See link, if you look in some of the pics, you will see stain on the walls, that's how fast they were moving.

Here is a link that might be useful: Stained and painted windows.

Appreciate the info and the link, looking at your project really helps.

That is a beautiful house! Congratulations. You must add a picture if it to the thread after completion, which it may already be.