Megatron was "Mega" from "Megaton", you know. "Tron" was from "electronics". I can't say for sure, but my belief is that that name became one of the best known. I remember it was in Doonesbury where the son of Doonsbury is saying that the President is Megatron or something like that. I think it's the best known and regarded among a lot of the names I came up with. At the time, Hasbro actually initially rejected it, and the reasoning was "Well, it sounds too scary because Megatron makes you think of nuclear bombs." and I said "Well, he's the head of the bad guys, the whole idea is for him to be scary." They dropped their protest after that. They would reject names every so often for all sorts of reasons. Although they were really happy, I mean they were just ecstatic generally when I came up with a batch of names for them to look at.

I think Bob Budiansky and co were looking for cool/heroic/dangerous sounding names and had absolutely little to no idea about the Greek origins of megas.
We've just assumed that they must have an existing point of origin & went looking accordingly.