If it wasn't connected via PCIe how would it talk to the GPU. Anyway Proxmox does in fact not officially support ARM so that is a pretty miniscule use case. I'm not even sure why you would want Proxmox on a low powered device.
For me PCIe pass though is the easiest. Virtualization adds little overhead in terms of raw performance so it isn't a big deal. If you prefer LXC that's fine but my initial statement was based on my own experiences.