Using a second window is probably in the same vein as using an external program. Glitches that can be used in a speedrun have to be achieved by the player without manipulation of the program, just the inbuilt physics and mechanics
"While recording runs, interacting with the game other than through the gameplay itself is not allowed. This rule covers both passive methods (such as RAM-watch) and active methods (such as removing or altering a game disc/cartridge/file while the game is running)."
So it depends on how this is achieved