I have to calmly tell it "laptop=this is not a laptop" and then it works as usual. I don't remember ever having to do this before. Why? If I have a clue I can code up and submit a patch.
This happens if flashrom can't identify the chassis type via SMBIOS (type 3 table IIRC). Basically, it assumes that if the user is on a system that is likely to have an embedded controller (typically laptops) then it is unsafe to proceed since ECs often share the firmware ROM and may interfere with the update process.
So if you can fix SMBIOS to indicate that you are using a desktop board then flashrom shouldn't bother you with that.