After fighting a group of monsters for the first time, Kiefer says that it's his first time fighting monsters. Caravan Heart comes out, and this makes it seem like a plot hole... but Kiefer didn't fight in Caravan Heart, his monsters did.
Gabo's joining level is a form of Gameplay and Story Integration — he joins at level one and doesn't have a lot of fighting prowess. Of course he doesn't — he is essentially a child and a feral child at that. Similarly, Melvin's starting stats are also rather fitting — he's been sealed away for God knows how long.
Dharma Temple is That One Level for a good reason: Orgodemir knew that it, more than anywhere else, is where anyone who could potentially fight against him would be able to maximize their potential and take it down. Knowing he was actually afraid of the place, of course he would send some of his strongest minions to take it out and keep it locked down as much as possible.
In Disc 2 when Orgodemir seals off most of the world? The levels sealed off are all homes to the great spirits... and Dharma/Alltrades Abbey for some apparent reason. Acceptable Breaks from Reality? Partly... and to keep people from class-changing to warriors to fight him.
When you have to bench a party member, the excuse behind the Arbitrary Headcount Limit is that the skystone only fits four people. This may seem like an Ass Pull... until you realise that, at one point, only four people ever were in the skystone at once. When the group goes to the cathedral of light later on, Maribel is not with them (Donald instead takes her place) and neither is Melvin since he is already at the cathedral himself.
But Crispin rode in the Skystone with you - it's easy to assume that's how they know that it's barely big enough to have more than four people inside it. One of you was probably absolutely cramped.
While it seems as if only a few NPCs ever seem to have acknowledged things in other "past"s (the Torban player who descended from the Deja/Roamers, the old man and the kid from Dialac/Regenstein who warned Verdham/Greenthumb Gardens about the grey rain, someone mentioning a frozen ship in the past, the offhand mention of "tourists" in Engow), but one that almost everyone missed: The priest from Labres/Vogograd was actually encountered before the rest of the village, obviously playing Labres/Vogograd's scenario (and by extension Dune/Al Adid, which is to the south and can be accessed via the woods) further in the past than that scenario was. So given all you did for the priest, why wouldn't he remember you? He has amnesia. This is actually some meta-fridge brilliance wherein you realise that he could have spoiled several crucial plot details like mistaking Maribel for Aira.
Or maybe he actually did recognise our heroes once he regained his memories - this is why he locked them and Caleb in a basement where they wouldn't be killed by monsters. Either he knows the heroes can save him, or he is trying to do one last thing to show the heroes thanks for what they did.
Why do the portals look so familiar... oh, that's right, they're what Travel Doors look like in a 3D world!
