Looking through all of this, my own theory is "grotty hack". An extremely capable programmer, with access to all kinds of toys. Doesn't want to write or improve a world-beating document formatter, just get the document printed.

You can justify paragraphs easily enough with a simple program. As for the sub/superscripts, why not just annotate something like blah[up]blahblah[up]blah[down][down] etc. and then do a hacky preformatter that sorts all of this into microspaced lines. Print the stuff at each height in one pass, go down a microstep, print the next and so on. He did have a Selectric-type machine available driven by a computer in his basement after all.

What do you do with a grotty one-off hack once it's done its job? Bury it. Don't mention it in a workplace full of geniuses who would write something like "troff" just to make a point. Especially because they did do that only a few years later. Doesn't solve the mystery of why he didn't bother to go through with the PhD of course.