Well, I wouldn't say it's BS, but in most cases it really won't make any difference as long as the application is the same. If you need GPS capability, you make sure the antenna has integrated GPS like the APX antennas do. If you need coverage from 440-470, make sure the antenna you're using covers that spread. Otherwise no, it's not really going to matter all that much.
I've been using an XTS UHF whip on my XPR 6550 for years, and it works better than the stock XPR antenna, and is much more flexible. Likewise I've got a VHF APX antenna on an XTS 5000 and performance is equal or better than the stock XTS antenna. I've even used XTS antennas on APX radios (no need for GPS) with no discernible impact on performance.