The article compares "clean" insertions and deletions on paper with commentary "piled up in the margins" from tracked changes. Yes, marginalia is more foreboding than a simple strikethrough, but that's not a digital vs. hard copy issue.

Comparing apples to apples, the deletions and insertions in track are just as visually simple as on paper. The article's suggestion of more in-lining, if applied to comments on content from multiple editors, would be a nightmare. You wouldn't be able to fit some sentences on the screen; they'd be crowded out by all the interruptions.

The article also complains that small punctuation changes can become tedious. That's also true in either form, and the solution is probably organizational. You can reserve a punctuation (and S/V agreement, spacing, etc.) pass for right before publication, or just have a standing agreement that minor cleanup needn't go in track (just accept those yourself as you insert them).

I feel like the most significant failing of track isn't when comparing it to paper. If you're widely circulating a doc for comments, merging edits from a dozen commenters is its own special form of hell. That's true on paper, too, but not in editors that allow real time collaboration, like Google Docs. (That's admittedly a tradeoff, depends on how much you want a single individual acting as gatekeeper for all changes.)