I've done the music list for my Captain Falcon stage submission on EAC tomorrow in advance, and I originally had a licensed game song on it, labled under the TOP SECRET name Melee used for GoldenEye content - the only reason I rejected it was because it didn't fit the tone of the stage aesthetically, just the gameplay of the stage.
I think I'll be lax on licensed game content. As long as the game was developed or published worldwide by a studio involved with Smash (or is Disney related) and the content wouldn't make the source material instantly recognisable (no Big Apple 3AM since it samples the TMNT theme, sorry 'bout that), it should be fine, so long as you rename the content when needed