I couldn't help but notice this wiki seems to focus more on the information that slightly implies that the villains survived, and ignores the bigger evidence they're most likely dead. There should be a rule of the internet for this, if a villain dies, they deny it, and if they can't, they speculate of their revival. (Ronan, The Other, Chrysalis, Sombra, I've seen this before, but this seems to be strongest in the Sonic series)
People think Mecha Sonic survived because we see an image of him with a black screen after the credits, which is probably not canon. People think Black Doom survived because he claims to be immortal. People think Mephiles and Iblis survived because Mephiles turns up in the Archie comics which are a completely separate universe. People think the Ifrit survived even though he fell and exploded. People think Eggman Nega survived coz we never actually see him die, and that one I can actually say is reasonable because they could have him escape and bring him back. People think Dark Gaia survived because Professor Pickle says "It could be that the darkness was not destroyed", which can be explained that he is dead (rapidly decaying, green blood gushing, etc.) but his power still exists in a disembodied state (think Lord Darkar, although there is much less speculation that he survived since it was explicitly stated he was destroyed). People think Metal Sonic survived because he can still be found in the White Space for a rematch. And people think the Deadly Six survived because Eggman, who did not even witness the battle, said he'd control them again.
The only two villains who people believe actually died without question are Captain Whisker (due to his ship being blown up and the heroes saying "the pirates are gone so who could've stolen the Jeweled Scepter this time?) and Master Core: ABIS, since there is no way anyone can pretend he survived that nor anything to imply that he survived. Should I add that under their trivia sections? "ABIS is one of two villains to die in the series, other being Captain Whisker". Even though there are others on the list (besides regular Eggman robots) whose survival is unlikely and was never confirmed.
They are not Eggman. And Eggman doesn't survive the explosions, he escapes them somehow. Eggman is Eggman, he's always sneaky and manages to escape certain death or even imprisonment, and he'll never exit the series because he's been there for too long. But just because this applies to one villain who appears in every game doesn't mean it applies to one-shot villains.