ill try and post another build before the nights out- i managed to fix the first, the player isn't effected by the conveyor belt now, i don't know how i forgot about it but you're not supposed to stick to it, it's only because i'm using a physics-enabled player now.. there's a lot of things in this game i added years ago and just forgot about or only now realize don't play nice with newer things i've added since, so uh sorry about that!!
as far as the area transitions, is it only ones with teleporters? like the UFO or Pit or stuff? if so its probably just cuz the arms makes your characters trigger collider bigger, so the distance you spawn works fine if it's a normal size but not if you are already touching the teleport- if not i'll have to take a closer look, but i'll try to solve for the first part at least.