Hi @Ellu24,
LS1046A can boot from SD/eMMC. It cannot boot from SSD. So if you use SSD, you need to use some other boot source.
You are planning to use USB-PCIe bridge. I'm not sure why you do not plan to connect M.2 SSD directly to PCIe controller of LS1046A. This will give you very high throughput.
The USB controller of LS1046A complies with USB specification rev 3.0. You can plug-in anything that complies to the specification.
Regards,
Mrudang