Dan, I don't have much in the way of insights as what you've observed is correct. Milestones are unlike other timebox objects in that they have a single Object ID. Agile Central is able to apply project scoping more easily to Release and Iteration timeboxes because a Release that spans multiple projects is actually comprised of multiple Release objects. The end result is that none of the Milestone charts or detail pages honor project scoping. There are at least two relevant enhancement proposals in Idea Manager at
https://ideas.rallydev.com/ideas/D3426 and
https://ideas.rallydev.com/ideas/D3459 if you'd care to add your voice.
Meanwhile the best workaround that I can suggest (and it isn't a great one) is to Milestone-filter a Custom List with the columns that you'd need, export the results and do your analysis in Excel or your charting tool of choice. Hope that helps.