Yeah that glitch is something major.. The flags remain active between saves, and you can trigger events from entirely different maps provided the IDs are the same. I played around with it for a little while and it didn't take very long for me to figure out how to get my HP above 1200. =/
..It's actually kind of interesting, seeing what events you can trigger from where. I started a new game and accidentally triggered the island falling scene, so technically my record of finishing the via normal ending w/ 3HP is 15 seconds?
The audio and visuals for this game are excellent, but the programmers really let the whole team down.
Edit: I just spawned Omega in Arthur's house, then accidentally warped to that fish boss - and I was restricted to the left half of the screen /and/ locked facing left instead of right.