noob question before start do runs: there is a reason of why we must do d4 like final dungeon before final boss instead of rather than just do it the first time you visit?

Because completing Dungeon 4 triggers the ghost sidequest which stops you entering certain dungeons until it's completed which wastes time. So it just ends up being quicker to finish D4 last so he wont get in the way.

D4 also just happens to be conveniently placed between D7 and the egg.