Re the first point: stdio only offers one way to interact with users. stdio is what pulls naive designers into this trap - untrusted output sharing a channel with trusted decision input.
Deno should disallow arbitrary output on stdout/stderr. Even prefixing the lines won't work because control characters like ^H are sent in-band and can delete the prefix.
The "in-band vs. out-of-band" is nothing new. Worth looking up 2600hz, the signaling frequency of the US phone system way back when. Pick up a handset, generate a 2600hz tone. Suddenly you're talking to the call routing system. Only a few steps from there to free phone calling anywhere in the world. Call routing signaling should've been separate, out of band - but given the tech at the time they'd have needed extra wires for signal lines ($$$) so the tradeoff was made, risk accepted.
The phone system designers went for in-band signaling to save money. Deno doesn't need to save money by running less copper so my money's on naïveté. Which doesn't bode well.
And the rest of the points made.. well yep the author is on point - made worse by Deno developers publicly defending their wrong choices.
Thankfully there're great alternatives.