Fantastic, standing behind the work. Sounds like they'll put in a smaller pump if that's determined to be a good idea. And don't feel bad, their pain in this will make future work better, protecting future consumers.
There really is no such thing as an exact manual J. And a problem when performing a load calc after the fact is it's pretty hard to avoid bias of making the J fit the install.
See if you can get them to bring a blower door. If not, ask for the J analysis on both very loose and very tight homes so you have a range.
Brand isn't the cause of this problem. Carrier generally tends to be the technology leader (everybody's got communicating now). One notable exception I'm aware of, the Rheem mod was revolutionary (everybody's got modulating now).