First off, we need to define OEM.
Original Equipment Manufacturer does NOT mean Original Equipment. It just means this is one of the manufacturers that may have produced the original parts for Ford, but they are essentially an aftermarket manufacturer making their aftermarket parts available to the public.
In essence, OEM is not OE. Even Motorcraft brand is not OE.
While these factory pumps often came with glass filter housings, it's not carved in stone, and some did not. Either way, the aftermarket replacements, OEM or other, mostly will not. You may find some that do, but mostly they don't.
The difference would be in your sensibilities to originality. If you're certain that yours originally came with the clear bowl, and that's what you want then seek out one that has it.
Keep in mind that the main difference from the factory was engine flex on acceleration, and how close that glass bowl was to other components. If it was close enough to shatter with a worn engine mount, then they probably didn't come with a glass bowl from the factory.