Your strongest case is that CPU design might stop getting faster, but that doesn't automatically mean progress towards AGI must stop.
Smartphones sell 1.2 billion every year. Add in server, laptop, embedded chips, GPUs, TPUS - even if transistor density and process improvements stall soon, the amount of compute power on Earth is vast and increasing rapidly until 'soon' happens, and can still increase rapidly by churning out more compute with the best available process indefinitely after that. You haven't made a case that process improvements are necessary or that they are not going to happen, you've only said that they might be neccessary and might not happen. "All it takes is for public sentiment to turn a bit more hostile towards technology, and progress can stall indefinitely" - again, true in terms of process improvements, not true in general because we could potentially make progress towards AGI with existing compute power by changing how we organise it and what we do with it; at least, you haven't given a good reason why that couldn't happen.
> "In fact, one of the strongest counterpoints to the article's thesis is molecular biology, which has a remarkable amount of momentum and a lot of room left to run."
One of the strongest counterpoints is that human brains exist - there's definitely some way to get to human-equivalent intelligence, on Earth, within the laws of Physics, the energy and temperature constraints which exist here. Handwaving "what if AGI is impossible because of the laws of physics" needs you to make a case why the laws of physics are a blocker, not just state that there are some physical limits to some things sometimes.
Yes transistors are hard to make smaller but that is not the only option - we've developed stacked 3D transistors to pack more into a small volume, hardware acceleration through design for more and more algorithms (compression, video compression, encryption) to better use existing transistor budgets, we've developed better more cache-friendly and SIMD friendly algorithms, chips where part of them can power down to allow more power for other parts without hitting thermal limits. More than one S curve involved, not just one plateau.