I recently purchased a Masi Fixie Riser with a flip/flop hub (gearing on both sides) and brakes, but the rims aren't machined. Is this common on $700+ single speeds?
It depends on the fixie.
A lot of them don't because brakes are not cool among the fixie riding population (since they primarily want deep V rims to look nice and resistance braking).
As for not having machined rims, depending on what the rim is coated with it can be OK -- if its powdercoated/painted for example, it will be too slippery to brake, but annodized surfaces can be used for braking just fine. The rims on the Masi should be annodized so you should be good for braking.