"It's very similar to an Fm."
Sounds the same to our ear, yes, and most people who play by ear or don't have theory training would hear that chord (or play it on their guitar) and call it an F minor. Hell, that's what I'd call it if I was showing someone else what chord to play. But in the key of C# (for instance), it would be improper to call it Fm -- you would call it E# minor, and you'd spell the chord as: E#, G#, B#, not F, Ab, C, as you would spell an Fm. Why? Well, I'm glad that you asked, and to be honest, a bit surprised that you even care, but here it is: It's because the diatonic major scale in the key of C# would be: C#, D#, E#, F#, G#, A#, and B#. Yep, 7 sharps, and you'd put all seven of them on the staff in your key signature when you're writing something out in C#. Otherwise, you'd run the risk of confusing someone who was attempting to sight-read the piece (by calling notes and chords by their enharmonic names, i.e. E# = "F", or B# = "C").
It'll still be kinda confusing to them, though -- that's a lot of sharps to keep track of on the page and on your axe. They'd probably be happier if you had written your piece out in Db, which would sound exactly the same, but have fewer accidentals to keep track of (Db has 5 flats, as opposed to C#'s 7 sharps). In Db, it would be legal and proper to call that chord Fm. BTW, the key of F# (six sharps) also contains the controversial and contentious E#.
Having said that, I'm guessing that Onstad referred to it as E#m just because he thought its oddness made for a mildly funny musical joke. Or maybe he just likes the damn key of C#.
Great strip, BTW. So very, very much to recommend about it.