The confusing listings are not Rockauto's fault; they're limited to what each brand gives them. However, I think I've figured out that the compressor itself (without the clutch/pulley) is the same, regardless of AT or MT. I happened to look at similar year Motorcraft compressor listings on RA, and they indicated that the clutch & pulley components are not included, so I think this one just fails to say they're not included. I also looked at TascaParts.com, and it shows that the compressor is the same but two separate options for the pulley. They also show that the compressor/clutch/pulleys are all discontinued, so it seems the dealership may not be an optional source.
I will say that I put a new Spectra Premium (correction from GPD; hey, it was 9 yrs ago ) branded compressor in my 1994 Ford Ranger one time, along with replacing all the hoses and other components, except evap,(which I flushed), and had awesome results. I think some people often just simply replace the comp, and when it fails prematurely, they get on the forums and blame the brand.