Ford sets the specs. Purolator is capable of building a filter to any standard. The standard they choose to build their Purolator branded filters to isn't going to dictate what Ford tells them to build and put the Motorcraft label on. I have no problem using them and do.
I stick to the FL400S because I know it will have a silicone ADBV (that's the "S" in the part number). Less than $4 a filter helps too.
FWIW, I don't trust everything Purolator either. I will not use their air filters. The gasket in my application for Purolator Classic and PureOne is too thin to seal the air filter housing correctly. I would absolutely use a Motorcraft air filter, even if Purolator makes it, because Ford said "the gasket WILL be this thick."
I trust Motorcraft branded parts. I have never gotten anything low quality that was branded Motorcraft. AC Delco can be a little more hit or miss, and if I had a GM, I'd source "GM Genuine" parts first. AC Delco filters are fine, but with things like starters or alternators, if there is a different "GM Genuine" part number from the AC Delco number, I'd rather get the GM Genuine. It can be hard to tell what's what with AC Delco, but Motorcraft is pretty consistent and reliable.