You have well summed up exactly where we disagree.
Either you have a problem with the wires next to each other, or you do not. Whether whte THHN wires are loose, inside a pipe, with the thermostat wires, or wrapped in a jacket and called "Romex" won't matter - at least not in a technical sense.
Look to your specs for running CAT-5 data circuits. That confirms thi point. There's a situation where there's a problem with 'low voltage' being close to 'power.'
As for the thermostat and it's associated air conditioner, I think the code, and Webster's are pretty clear: There's no such prohibition, and the cited section does not apply.
Unless, of course, one wishes to maintain that the code is absolute, arbitrary, and it's words defined only by the convenience of the moment.