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Just as an update for all future readers. I have chosen SAIS as I had to submit my deposit today to retain the scholarship.
@kd7432 Hmm, well frankly I'm not sure. I didn't apply to any of those schools because they didn't seem to have what I'm looking for. It seems to me that Georgetown MSFS is king when looking at area studies (I really don't know about McCourt). Since you're looking to do a PhD as well, have you tried to see which program would give you the opportunity to prepare best?
On a personal level, I wouldn't want to live in Michigan or North Carolina, so I'd most likely choose McCourt... but only you can really know if it's the best decision for you, I suppose.

I know two people who graduated from SIPA and are now pursuing PhDs - one in poli sci at NYU and the other in econ at Berkeley. I am also considering a PhD later and was looking at SIPA. Both told me that SIPA allows you to take PhD level courses, and suggested that I take real analysis and advanced micro at the very least, if not more of the math/higher level econ courses. Check if SAIS will allow you that. 
Plus, for a PhD you will need excellent recommendations. So you should see wherever you can get more interaction with faculty (through RAships, TAships, office hours etc.) and where there are more faculty members in your area of interest.

It might be different for the IDEV program, though. HKS' MPA/ID, for example, is quantitatively rigorous even though the MPP can be completed with little quantitative rigor. That said, I'm not familiar with SAIS' IDEV program, so it'd be great if someone with more knowledge of the program can step in here.

For what it's worth, I interviewed lots of former and current SAIS students during my decision process and everyone said the Latin American Studies Program is almost bizarrely well-funded and managed.
I was also told (and again I have no first-hand knowledge of any of this) that SAIS' econ courses are not particularly rigorous for those with undergrad econ educations. Again you should take this with a grain of salt, but I'm not sure SAIS econ requirements would necessarily prepare you for a PhD.

In my non-expert opinion, the quantitative/economic rigor of SAIS' IDEV seems like the obvious choice given your goal. Economics PhD's are heavily quantitative (as I'm sure you know), so you'd be best served to go to a program that will best develop those skills. Based on what I've heard, it sounds like you should also take multivariate calculus (and probably linear algebra) if you haven't already.
Finally, I do not think it's correct to consider pursuing SIPA's MPA and pursuing HKS' MPA/ID as both being on the "Chris Blattman route." The latter--which is what Blattman did--is much more advanced quantitatively and requires multivariate calculus for admission. Blattman said it came close to what would be expected in the 1st year of an econ PhD program.