I use myTracks to extract a GPX file, and then use either exiftool or Aperture to tag the data. As I'm often using exiftool to add manual-focus lens metadata, this isn't much of a pain.
It turns out that Aperture isn't rounding the data as I had thought, but I was getting poor results because of how I was aligning the track to the photos. There's no easy way in Aperture to actually use the timestamps without adjustment. Ironically, this means you get better results when you align using a point when you
were moving quickly.
I was trying to align the track at my starting point, you get better results picking something in the middle.
Exiftool, as you'd expect from a commandline tool, allows precise control.