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It doesn't matter how many episodes a producer wants, if the company paying for it wants to cancel before or add seasons they will do it. That's why we have many shows that end with cliffhangers, and shows that had a series finale and yet have another season or two even though most things had been wrapped up.
That's why most shows leave finales with some plots here and there so that they can work as a series finale and yet can still continue making new episodes. The OT had plenty of those, 2k3 meant to continue but they gave us the wedding "just in case" which was good. I'm sure if Viacom had said "one more season" then we would've gotten another season of "tales", and also that they weren't sure if they were getting season 4 which is why we got Shredder's defeat there and then, they might've thought it was their last season and were surprised to get a fifth one, it's logical since even S5 only got 20 episodes instead of the usual 26 that the show as used to.
As far as the mutagen bomb, I don't think it was ever meant to be explained, even though it's meant to be in continuity that episode was kind of done as an elseworlds story or alternate future and not to think much about it. An actual episode telling the story of the mutagen bomb would likely be boring. It's like in Star Wars, the idea of a prequel of how things got that way was cooler than the actual prequels, it's hard to tell those "prequel" stories that are hinted at.
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