In today's review of the X-Men Marvel Legends "Age of Apocalypse" Morph, we talked about how the character's inclusion in the crossover was inspired by the cartoon. But the inspiration runs both ways.
X-Men the Animated Series was never above adapting its episodes from classic stories in the comics - it managed to do the entire Phoenix Saga better than two movie attempts, for example - and at the beginning of Season 4, it tried its hand at the Age of Apocalypse.
The two-part "One Man's Worth" aired in September of 1995, mere months after the crossover had actually ended in the comics - given the huge production time for a single cartoon episode, the writers must have gotten wind of the idea almost as soon as the X-Office at Marvel had started working on it. Which would explain why other than the broad stroke of "Professor X is killed in the past, changing the present," the plot of the two stories is completely different (and also why a two-parter is so jammed with repeats and recaps that there's barely enough material for a single episode in there).
While the TV show's script would have to be locked down pretty early, the character designs would have had a little bit more flexibility, which is why those were able to use (rough, hastily created versions of) the AoA comic costumes for background characters - including a scene where we see Morph sitting sadly on the ground after a battle.
So we have a situation where the cartoon took inspiration from the comicbook storylines, then the comicbooks took inspiration from the a character the cartoon chose to use, and then the cartoon took inspiration from that character for their character. And then later in the episode, someone who appeared to be the normal human version of Morph also appeared, wearing a different costume in a scene that had obviously been animated sooner in the process.