The "allowance" notion vs. firm quoted budget is important to understand. Your engine is supposed to be a standard rebuild and they open it up and something unexpected isn't good. New part is pricey and/or hard to find.
The other aspect is the changing of the scope of the project mid-stream. Many shops love this upsell. How many Hot Rod Magazine articles start with "I was just going to do a driver, but then we got it all apart and..."