ZellyV:

Have your contractor explain how he will detail these transitions. I doubt there will be any damage.

You should be fine

Do the new units have the exact same rough opening?

The window and doors will be the exact same size.

If you are not getting siding replaced you will likely have "replacement windows" which are put into the existing frame and the inside trim is unchanged.

I had a "new construction" window put in because my siding is being changed, they had to change all the inside trim also but used the silhouette of the old trim on the wall to exactly duplicate the location of the new trim. Pretty sure they could have done it without damaging adjacent structures.

When my replacement patio door went in they used the same RO so that the outside part that overlaps the siding was untouched but they did replace the inside trim with a much more substantial trim that better matches the size of the door. I can't see that it affected the inside wood floor , and tile would be more damage proof I would guess.