I'm trying the transfer again. I went through and deleted my existing audio files in the handheld sync folder.
It seems like the time-to-completion estimation has changed. It is a LOT more optimistic early on than it was before. When I did my tests earlier today (with the previous build), it would generally list 2-2.5 hours to completion pretty quickly after starting. It wouldn't actually ever take quite that long (though it would take a long time, and much longer than it would take with a direct connection to the library). It would generally get down to around 1 hour remaining, and then would suddenly jump to complete.
This time, it started off listing 18-20 minutes. It has been running about 20 minutes, and now it lists 58 minutes remaining. That's actually more in-line with what I saw with directly connected syncs, though still maybe slightly slower.
The bitrate throughput listed fluctuates a lot, but generally seems substantially higher than it was with previous builds, so I think it is actually doing the sync faster. With previous builds, I was seeing typical speeds of 60-80MB/s, with occasional fluctuations up to 100MB/s or so (and occasional stalls down to 20-30). Now it seems like it is staying up around 100MB/s a lot more, and fluctuating wildly (often showing as high as 160MB/s). Of course, it always slows way down when it has to actually convert a track, and is fast when it can use a cached or direct file.