Yes, the incompatability of modern hardware is likely to be your main problem. However, I still have the PIII system and QNX and Amiga OSXL is still installed on it!
Because you already have a working copy of QNX v6.4 installed, I will concentrate on describing the installation of OSXL into the QNX environment.
I am not at all familiar with virtual machines, but I suspect that the compatibility issue will still be a stumbling block, unless the virtual machine is capable of some degree of emulation of older hardware.
[Edit] I was also going to suggest that you read the Amithlon Setup Guide thread, but I see that you've already found it.