Extra Masters before PhD In my field it is common for Americans like myself to do a 5-6 year PhD where the first two years are basically a masters degree. However, when I first applied two years ago I was rejected from all PhD programs and instead did a free-but-unfunded MS. Now I am applying again and got an amazing offer from a top 10 US program! If I go there, will it look bad in post doc/faculty applications to have a 4 year undergrad, 6 year PhD(+MS en route), and a separate 2 year MS in between?

I am also still being considered for funding by the very top non-US program for a 3 year PhD where a MS is required beforehand. I had initially thought a longer PhD was better in order to do more research and make more publishable discoveries. But is the potential CV oddity worth considering if I get into this other top program?
No, given everything else you say, no one will give it a moment's thought. You've been on a steady path and seem to be a success at it. 

And, almost any other option will be worse. A different doctorate would shorten your time to completion, but, as you say, this one gives you opportunities. 

People will look primarily to your most recent accomplishments in any case. It is just how it works. 

Just. Do. It.