This one should be top comment.

In the Song Exploder episode, Marshall recounts writing the initial chord structure, themes, narrative, and main melody (most of which remained in the final iteration.) The main thrust of the song had to do with a toxic ex-gf Marshall had.

Then Phoebe talks about when Marshall first showed her the song, him not thinking very highly of what it was, but Phoebe could see its potential immediately. She took the song and improved on certain aspects and finished what was incomplete (like remaining stanzas). For example, the whole “do you feel ashamed” was all Marshall’s, and Phoebe kept him from adding “I hope you do,” etc.

The rest of the episode describes the recording process with Tony Berg.

In conclusion, the song is not about Marshall so much as it’s a song that Marshall started and Phoebe finished.