If the software uses PCI methods to detect the GPU (e.g., nvidia-smi), then there is no possibility of any auto detect working. Unlike a PC with a PCI bus GPU the integrated/iGPU of a Jetson is directly wired to the memory controller (the driver has no PCI interface query possible for the iGPU).
Seems that I am stuck with Jailhouse, I’m moving to Xen for this. Still, if anyone is ever able to find a working solution for Jailhouse I would appreciate an answer.