I couldn't find anyone else doing this, so I'm posting my solution for FCP originated native AF100 conforms.
It revolves around a program called ClipWrap, which is a quicktime wrapper (not transcoder) for .mts files.
1. In FCP (or Avid) build a list of your AF100 media names. (i.e. from "reconnect media".)
2. Search in finder for .mts
3. Select and drag those clips into ClipWrap from your clients drive, and set the destination to your local RAID. Make sure its set to re-wrap, not transcode.
4. ClipWrap will build quicktime files as fast as your drive can copy them.
5. Assuming your client didn't rename their prores files, relink in FCP or dump direct into media pool.
In the event that you have a longform project, and there are too many source files to copy by hand, the following (untested) workflow might work:
(note: I have only cursory knowledge of premiere)
1. In FCP, build out a timeline of AF100 only clips.
2. Export an XML of those clips.
3. Import the XML into premiere pro.
4. export a trimmed copy of the timeline (essentially media managing to trimmed .mts files.)
5. Dump the directory of trimmed .mts into ClipWrap and spit out new trimmed quicktimes as above.