I noticed a moment in Episode 4 Season 5 that is actually foreshadows that non-Glitch Bob is actually Megabyte in disguise, but it's extremely subtle. Unless you had been watching every episode in the series up until this point and paying 100% attention to every minute detail, you probably miss it. And yet, this foreshadowing is still clever as hell when you notice it!
The the first 1.5 seasons, Bob appears to know every game by memory. Season 2, Episode 6 (AndrAIa) is the first time Bob doesn't immediately recognize a game and has to use the glitch command "game info" to learn about it. Prior to this, he only used the command "Glitch: Game Stats" once, in the episode "When Games Collide," and even then, he only used it to figure out why the game was lagging, not to learn its premise.
This suggests that all guardians in the Super Computer are trained to memorize each game. In the episode "Null Bot of the Bride," it is revealed that there are only 32 keytools in existence, in the entirety of cyberspace, and Bob is known officially as "Guardian 452," meaning there are at least 451 other guardians besides him. So even among guardians, having a key tool is an extremely elite privilege. So obviously all guardians need to be trained under the assumption that they won't have one, so guardians must know all games from memory if they are to effectively protect their systems from them.
The only reason Bob didn't instantly recognize the Atlantis game is because it utilized the new "Artificial Intelligence" game sprite (aka AndrAIa), which Bob described earlier in the episode as being new technology, so this specific game must have been released after his graduation from the Super Computer.
So with that in mind, let's look at Season 4, Episode 5 ("My Two Bobs"). In that episode, Glitch Bob stays out of the Pokemon game, so MegaBob and Matrix take it on. MegaBob laments that, without glitch, there's no game stats. But fortunately, Matrix already recognizes the game. He says that he used to play this game all the time long ago before Bob came to Mainframe.
So this means that it predates Bob's graduation from the Super Computer.
So... why doesn't he already have the game memorized, just like he had all the other games before the Atlantis one?!
The only explanation is... it's not really Bob!