Thanks to the efforts of the runner Nobobin. He has discovered after going back to the Squid Sisters Camp when defeating Grizz/watching the Credits, that due to performing Switch Skip. (An Out Of Bounds skip performed in Intermission Phase 1, which skips Phase 2, Intermission Phase 2, & Phase 3) The game will not actually be treated as completed thus not allowing the player to unlock and play After Alterna. Once going back into Rocket you can skip Phase 1 from the pause menu, (due to the fact that you completed it) but will have to complete Phase 2, Intermission Phase 2, & Phase 3 as a result of performing Switch Skip. Once you load into Intermission Phase 3 a strange thing will happen that I will link down below:

Essentially the game thinks you are loading in from the invisible Rocket kettle that you normally load into. This is located under the map. You are frozen in the air for a bit while coming out from the kettle, you drop to the ground while still frozen, the textboxes start playing for the start of this Phase, the game autosaves, you get the power egg bonus from completing all of Rocket, then the text box appears confirming that you unlocked After Alterna. Once you gain control again simply pause the game then go back to the Camp to play After Alterna.

P.S. The reason why Menu Storage still allows for unlocking the Post Game over Switch Skip is that for a Phase to be treated as "completed", you must either play the entire Phase, or select the Skip option in the pause menu. Regardless if this is through Menu Storage or from a NG+ file. Due to Switch Skip not setting the flag to complete in Phase 2, Intermission Phase 2, or Phase 3 they will not be treated as completed. Thus having to go through the steps described earlier in this guide post. Due to all of this being slower for a speedrun, it will not be banned. However, do note that when running All Missions, 100%, or 200% that you should not perform Switch Skip as it loses more time than it saves. Also, for All Missions NG+ Switch Skip is faster as it doesn't suffer from the same restrictions as the NG categories do.