At first glance, the naming convention of the Canon MP-E 65mm 1-5X Macro lens seems to offer us a clue. In the case of the MP-E 65mm the "MP" stands for Macro Photo. The lens is not designated as an "EF" lens because "EF"stands for Electro-Focus and not only does the MP-E 65mm not have a focus motor, it also only has a single focus distance at any given magnification ratio. So is maybe a PE lens a non-Macro fixed focus, or at the very least non-AF, lens?
Not so fast my friend! The PE 300mm f/1.8 does appear to have electro-focus capability as there are focus limiter switches visible next to the focus distance scale.
Canon once sold a rangefinder camera model named the "Canon P" that used the Leica M39 screw mount (LTM). It was introduced in 1959 and was succeeded by the "Canon 7" which was the last M39 rangefinder Canon produced. But this PE 300mm f/1.8 lens is obviously not used for a rangefinder system as one can see there is a viewfinder jutting out at a right angle to the optical axis on the front of the camera to which the lens is attached. This is another image from the PetaPixel article.
Although there have been anecdotal reports of rare sightings of Canon "PE" lenses, the images attached to the PetaPixel article are the only photos I've ever seen of one. Canon seems to not want any information regarding any such "PE" lenses to be public knowledge. This might be related to the fact that most (very rare) reports about PE lenses indicate they are generally sold to government and law enforcement agencies involved in sensitive information gathering activities. Such agencies typically do not want their "clients" or competitors to be aware of their exact surveillance capabilities.
Based on the rarity (the user of the lens featured in the articles says there are only four copies that he knows to exist), the large optics involved, and the fact that most PE lenses are sold under classified government contracts,
I think PE can probably be interpreted to mean Prohibitively Expensive!
Alternate possibilities for the naming convention:
PE = Physically Enormous
PE = The class required as a prerequisite to be able to handle this one
PE = Prototype EOS