Well... I think I just see them as two separate issues. Your point is 100% valid but I'm not sure it undoes any of the argument about progress on fundamental research; I just see them as tangential issues.
Like, we're still exploiting people and the environment of the global south. That didn't go away (in fact we arguably got more efficient at it as the systems became more refined and less go-in-with-gunboats brute force). But for some reason the progress in base research did go away, and he's trying to get to the reasons why that happened. If we'd actually undone colonialism but lost progress in basic research as a consequence of that then yes; but I don't think that's how it happened.
The point that, he shouldn't be thinking only of good scientific progress in the wealthy sector of the first world and everyone else isn't real important, yes I 100% agree with. I also think it's not strictly an either-or though -- the same systems that are screwing a highly educated person in Idaho who can't get funding for their good idea, are the same systems screwing the Honduran farmer. If getting to the reasons behind (a) are going to lead to shedding any amount of light on (b) via some further investigation then I'd be in favor of that.