To not lose sight of the discussion subtleties, the gp was saying that in this 1st scenario, Bob still didn't "solve it (totally) on his own" because he still depended on the previous work of others to build on. Likewise, we can say Andrew Wiles "solved Fermat's Last Theorem" but Wiles acknowledges that seeing Ken Ribet's proof of epsilon conjecture was a breakthrough he used.

>In another, Carbon-based Charlie breaks into Bob’s lab, copies enough of Bob’s notes to understand Bob’s work, and provides the final insight to solve the open question. In this world, it’s fair to say that Charlie and Bob both contributed to solving the open question, but I think also fair to say that Charlie didn’t have the capability to solve it on his own.

Again, using gp's framing, Bob also didn't have the capability to solve it on his own. By omitting the previous papers and prior works that Bob built on, it makes your hypothetical scenario incomplete when judging Bob vs Charlie.

We don't have an objective standard of how much the "standing on the shoulders of giants" applies to each breakthrough. There was a blog post (might have been Terence Tao) that said society unfortunately awards the fame to the person who solves the last step of a proof and forgets about the people who solved the intermediate steps that led up to it.