It's honestly common across not just JRPGs of the time, but cRPGs in general across all eras. The endgames are a. content that the people making it *know* won't be seen by as many people as the start, b. the people who get there will already be dedicated to finishing; c. need to be challenging on a mechanical level.
So you tend to get monster gauntlets and extended-length encounters (hence the classic multi-form boss) because those are easy ways to add difficulty. Consider KotoR's Star Forge sequence, or the Mass Effect 1 & 2 end sequences, or CT's Black Omen, or Phantasy Star IV's Rykos, or Pokemon's Final Four, etc.
They can be impressive in their own right for other reasons, but they do tend to be of the 'let's throw a pile of our hardest enemies at you' school of design, as both a sort of vibe-check of the player's preparation and a means to attrit their resources before they hit whatever the final fight actually is.