not if the original game calls for fighters\poketrainer\ which isn't used in PM
I think that's why it states, you need to do a normal match first for some cheats to apply (changing the call for fighters\poketrainer\ to something else)
I can't test it right now, but maybe can you or someone else test, if you can play subspace emissary completely while making sure to follow this?
The Subspace Emissary
SSE is now playable, but has several avoidable glitches.
-SSE now uses normal attributes
-Before entering SSE, some codes need to be initialized by starting a regular match first. Most notably, Dark Ice Climbers in The Great Maze will crash if you don't.
-Certain reflection, such as Ganon's, don't work.
-The turbo item sometimes gives both the turbo and curry effect
-Certain Physics codes, such as being able to wall jump on the same wall twice, are not active in SSE
-Galleom and Duon use Mewtwo's and Roy's soundbanks respectively.
-Pokémon Trainer related glitches:
--Pokémon Trainer is listed as Mewtwo in the menu.
--Squirtle can't switch to other Pokémon.
--Using a costume over the default Pokémon slots (particularly Squirtle) can put the player over the memory limit and crash.
--If Kirby is in your party when you fight Dark Pokémon Trainer in The Great Maze or if Pokémon Trainer is in your party when you fight Kirby in The Great Maze or the Midair Stadium, the game will crash.
--In 2 player SSE, if Player 2 is Pokémon Trainer, Player 1 cannot interact with doors properly.
--Dying as Pokémon Trainer in certain fights can cause crashes.
Edit: I added compatibility to Project M Patt Edition 3.5-01 to the batch file, I will attach the file here, but you can also get it from the first post, I edited it in :-)
also added some new checks, so that it will now tell you, if you are using an invalid and scrubbed .iso