It's one of those topics that are bound to be a bit tricky, since the story concept of PULSE was created before Megas, but the current mechanic only afterwards. So originally, the idea was really just that Eve decided to build a machine to power up Pokémon, no mega evolution involved. But now that it does exist in canon, it wouldn't make sense if megas hadn't inspired it in-story^^
Out-of-story, though, it does predate megas. It just worked differently in the game back then and was adjusted later, because the mega mechanic was perfect for it, really. (I think it's funny that you bring up Porygon. The guy who came up with ZEL told me once that he thinks it would make a good choice for Eve's team despite not even being a Psychic type.) Edit: For a couple of fun facts, though:
The PULSE idea was created specifically to make a backstory for ZEL. The characters were there first, and only when Ame wanted to use them for the game, she discussed with the creators of the Meteor characters what would make a plausible explanation for how the three ended up fused into one body.
So they eventually came up with the idea that it was an accident during an evolution experiment. (Ditto/a DNA fusion experiment was considered briefly, too.)
Naturally, then, there also needed to be a backstory for why the experiment was conducted - resulting in Ame writing the story you read in Lumi's diary.
So technically, PULSE only exists to explain ZEL, and conveniently turned out to be a neat story element for the game as a whole.