As said, buildings build and placed by other mods, eg Quantum Fabricator aren't counted by Milestones.

I would have to take a look at the specific case to understand what the player experience is supposed to be, but as a general case if a mod is producing things "on behalf of the player" it should also probably add those things to the Factorio production graphs, at which point Milestones would detect it.

Does that fit here? Or does this mod do something different that would still be worth tracking via Milestones?

The mod has an infinite storage, which stores your intermediates and then fabricates the buildings and places them at an instant. Technically they are produced by the mod.

Looks like they fixed it on their side.

https://mods.factorio.com/mod/quantum-fabricator/discussion/687e86ace9d4750394d8d3a1