This is the part of a painting project people dread, so it is worth being plain about. Some rot is only visible once the old finish comes off. When that happens we stop, show you what we found, and price it before we carry on — it does not get absorbed silently and it does not appear as a surprise at the end.
You can also say no. Painting over it is not what we would recommend, and we will tell you what we think it costs you later, but it stays your decision and your house.