Most surface-mount USB connectors will have small plastic nubs for alignment, but unless you're using some crazy-thin PCB the won't stick out the underside.
Yeah, the ones I'm using now have them, but those are less than a mm in length and are zero-force-insertion, so they don't require another step after the pick-and-place process.
You need to redesign your product, or it will fail.
I'm looking into alternatives. Some of them have SMD leads but anchor their frame to the PCB, like this one:
http://il.farnell.com/amphenol-fci/87583-2010blf/usb-2-0-type-a-receptacle-smt/dp/1314363Can those be placed by a pick-and-place machine, or do they have to be snapped in manually? I assume they require manual soldering if you want those anchors to properly bond with the PCB, but can the initial placement be done with a machine?