Glitch is performed by activating a screen fade-out and then pausing, choosing "Restart" or "Quit" (yes, it works with the Quit button which means you can do it if you don't have lives for a Restart) and then pressing the pause button again in that order to unpause the game after a restart. Doing this has a number of weird effects.

As Milla, you can use the fadeout skip even on transitions where it wouldn't work normally, by holding a super shield burst while approaching the loading zone, waiting for the game's movement lock to recoil her out of it and performing the glitch before Milla enters it again. Avoid approaching the loading zone at a high speed, if you want to do the glitch, or else, the recoil won't push her out of the loading zone. This means, if you are approaching the loading zone at max speed, it's not worth going for the trick, even if it works.

Many of these need to be delayed until the screen is about half faded-out for them to work.

NOTE: Transition skips that need a delay to work might be dependent on the speed that you exited the room at to work, they're kind of inconsistent and fiddly.

NOTE 2: Doing any kind of fade out skip and then dying will result in the game thinking you restarted in the state you were at when you died. I.e you'll respawn with zero health and however much meter you had when you died. This isn't really useful anywhere and there's nowhere it can really catch you out in a run, but I just want that knowledge out there.

Dragon Valley:

Exiting first screen - Works, needs delay. Is a bit inconsistent anyway. Entering 2-2 - Will skip fadeout animation, but has to be delayed a bit for some reason. Saves a bit of time.

Aqua Tunnel: Exiting first screen - Works, but needs some delay. Exiting second screen - Works with little to no delay. Exiting third screen - Doesn't work normally.

Relic Maze: Purple/Yellow/Train Door/Transition to RM2.2/Big Round Door - Will skip fadeout animation and doesn't require any delay, saving about 0.7s each. Four places this is useful in, so net like 2.5s for F R E E. Neato. Going Into Autoscroller room - Appears to work and save time at first, but on exiting the room will act as though you restarted and reset both rooms. Useless but amusing. Exiting Bone Golem Room - Will skip animation but will lock the pause menu and prevent you from using it, which prevents you from doing the restart warp at that point, so it ultimately works out slower to do it here for Lilac/Carol. May be faster for Milla?

Fortune Night: Wrong Warps - Works, but has to be delayed slightly in order for it to count as a wrong warp. Saves a decent chunk of time, but not as much as the regular transition skips due to the need to delay it.

Sky Battalion:

Leaving Any Ship - Works, but has to be delayed somewhat for it to count.

Jade Creek:

Exiting Screen 1-1: Works, but only really for Milla if you bounce out of the load zone in a fashion similar to the Fortune Night Wrong Warps Exiting 1-2: Works, but only if you have good speed, which means if you botch the glide under the ceiling, don't attempt it because it'll just screw you over instead. Entering second sub screen after Neera/Exiting sub - Works but needs heavy delay.

Trap Hideout: Exiting first screen: Works, but needs some delay. Exiting second screen: Doesn't work normally.

Thermal Base:

After Box Zip/Entering 2-2 (the door after you get the fire shield) - Works, requires delay. Boss Room Entry - If the elevator has caught up to you, needs to be delayed to work. If it hasn't, requires no delay whatsoever. Actual time save varies as a result of this.

Pangu Lagoon: Exiting Screen 1 - Works, needs delay. Doors - Works on both doors, which saves about 1.5 seconds of real time but absolutely no game time and thus isn't actually very useful to runs. Race strats or some shit.

Battle Glacier:

Entering Boss Room - Works, needs delay.

Final Dreadnought 1:

None.

Final Dreadnought 2:

Entering second screen - Works, needs delay.

Final Dreadnought 3:

Entering hallway - Works, needs delay Boss Room Entry - Works and saves time, but only for Milla. It does work for Lilac/Carol but for some inexplicable reason will restart in the middle of the cutscene and ultimately lose time.

Final Dreadnought 4:

Entering Screen 2 - Works and saves time but locks pause menu, but the locking effect goes away by the time you actually reach Brevon, so you can still perform the restarts that save real time but no game time.