Why is that a mixed metaphor? I'm very used to large initiatives/programs with several large milestones, each involving multiple projects. I don't see any issue with it.

The milestone they are reaching is the formalization of The Stacks Project. It began whenever they started prompting an AI to do that or started preplanning.

The metaphor of milestone is a goal reached within a larger process. I think that, yeah many people will not find a problem instances of this sort of (mis imo) usage but AIs to create a sequence of these things and that tends to create a tone to AI writing that many people can feel even if they can't point to particular problem usage.