Magic isn't real.
In MSPA, magic is real. But in MSPA, said magic isn't called magic. It's how the universe works, so why would it be called magic? Imagine being in a universe where nothing burns. You come to our universe and see fire. It's magic! But we do not call it magic, because it is not abnormal for us.
The world of MSPA works quite differently from ours. Why would we explain "magical" things in their world with our science?
But no, no. Even that doesn't quite get it right.
It's a story.
It's not real.
You cannot come up with a "most likely" explanation, because it's quite probable that no explanation exists. This universe is contained within the mind of Andrew Hussie. If he has not bothered to think of an explanation, there is no explanation.
Imagine if Andrew Hussie were to write "These kids are all 13 years old", and then in the next panel write "The 31-year-olds get on the boat". Would you then say "The most likely explanation is that the kids went through a time portal which aged them 18 years, because we have seen that time portals exist etc."? No, that would be silly - it was a typo. No in-MSPA explanation exists, and it is the same for the troll universe and time travel.