When we quote advertising and fashion jobs there is an expectation that the final product will need to have a lot of polish and style applied in post, that's just how it is these days. For me that's also a big part of the interest, it's what makes it engaging for me, not unlike colour grading in film/motion.
The nature of our projects means most of our shoots take anywhere from 1/2 day to a week to execute 1-12 shots. The post typically takes longer then the shoot. We do not accept projects unless we do all the post and we expect a lot of requests, we expect to be asked to make magic and we plan for it because that's part of why we get hired. I can't help but note a bit of a peevish tone in some posts about lower rates and feeling put upon to do more retouching, consider improving your skills, or send the work out, but lots of retouching on commercial work is here to stay.
Recognizing the importance and respect of communicating boundaries in advance - giving the client the information so they can control their budgets and consider rates when they request changes, we separate the post into it's own area of the estimate, into the last section (we write in a chronological order of the project workflow).
In that section we describe how many final shots they get, the expected retouching based on our experience with our workflow and what we know of the project through discussion, scouting, experience, etc.,. All of this is included in the estimate, in an ideal scenario this would deliver the job for that price. Sometimes it does not, but that's the client's (informed) decision.
As an aside, I feel I have to mention that part of our job these days is to think ahead of our clients in a benevolent way, even my newish assistants know not to strike a shot until we've captured any number of plates to get background information, etc. To tell a client that removing a coffee pot is a big retouch because someone didn't capture a plate without it is a bit of a shortsighted approach to modern workflow.
Part of our estimate includes a time-cap on the post, on a per file basis. In other words 'for this type of shot you will get 60 minutes of actual retouching' (RAW processing and files finishing, draft proofs delivery, final delivery are separate areas in our estimates). In the event their needs go beyond this budgeted time we explain we will need to estimate the additional work as a separate fee, based on a transparent hierarchy of fees; basic at x and hour, more involved at xx an hour, difficult at xxx an hour. We bill additional work in 15 minute increments. The software we call on is immaterial, we are billing time and skill.
This method works extremely well for us and is in my view the most ideal and mutually respectful way to 'paper' the retouching portion of the agreement.
Hope it helps