I have switched hxcpp over from using ref-counting to using Boehm garbage collection. I have also added some additional perfromance improvements, such as integer-index field names to make interaction with neko more efficient.
The overall result is that for the Physaxe demo, the frame rate went from 24 fps to 82 fps (in opengl mode). The swf file runs at about 35 fps, and neko at about 8 fps. This is about what I was hoping for from the first round, but I got there in the end.