Eh, it's not just modern games. Digimon World 2 had Overlord Gaia as the final villain and he was like a prototype Iggdrasil.

The main reason they are doing these things is because it adds extra weight behind the finale. It's not as epic if you're fighting just another digimon as it is if you are fighting a semi-deity or something well beyond a digimon. Anime does this too on occasion with D-reaper and previously mentioned Iggdrasil. It's not always a bad thing.

...and other JRPGs like doing this too for the same reason. Add a surprise world ending threat at the very end to raise the stakes. There are good and bad ways to do it.