Yup, and even a custom builder is going to charge for change orders on a "time and materials" basis.
Part of the reason the builder in the OP's case is resistant is because this change involves an awful lot of work on their end. They need to draw up and submit new plans to the city/county showing the change, pay an hourly review fee for the change order, wait 2-4 weeks for the change order to process and be approved, pay the permit issuance fee, manage a second set of approved plans on the site/in the job trailer (oops, only the #1 set is here, no inspection for you today, try again next week). Then they'll have to abandon their existing mechanical permit for the FP install and apply for a new one of those for the ZC/woodstove installation. And that's just the extra administrative work involved.
This is a house that is likely being built in under 120 days from groundbreaking to final inspection, it makes perfect sense that a production builder would not make the changes you're asking for.
Builders in my jurisdiction hate going through the change order process, and they're all building custom homes that run $1200-2000/square foot to build, so it's a bit of a pipe dream to think that someone like Toll, Quadrant or any other national production builder is going to jump through those hoops for a client.