I just read through this topic (https://batocera-linux.xorhub.com/forum/d/139-great-job) but figured I open a new thread since I am using different hardware.
I am experiencing similar issues. I tried running Recalbox on my ECS PB01CF (http://www.ecs.com.tw/ECSWebSite/Product/Product_SPEC.aspx?DetailID=1732&CategoryID=12&DetailName=Feature&MenuID=40&LanID=0), a standard Intel Atom Apollo Lake x64 architecture, but unfortunatelly the integrated Atheros Wifi/Bluetooth Card does not work. This brought me to your build of Recalbox, batocera.
Out of the box, everything is running smoothly when using an USB drive. There is a microSD card slot but the BIOS is not able to boot from it.
I then installed batocera from an USB stick to the 32GB internal eMMC. Everything worked as expected but after a reboot, GRUB or more specifically INITRD was not able to find the internal storage. I assume that the proper driver is missing and therefore it cannot be found. When I use the USB drive to boot batocera, it will properly recognize the internal eMMC.
You said something about that modules are not available during boot and this is what I think is the problem.
Could you have a look at it?
You can see my lspci, lsmod and dmesg from lubuntu and batocera below:
batocera ( booted through USB )
lspci: https://pastebin.com/S33Wahi1 (only containing classes)
batocera (booted through eMMC, completed by inserting a USB drive with batocera on it)
When booting from eMMC, GRUB starts fine and loads the RAM Disk. However, the initramfs gets stuck when it is not able to find a partition labeled as RECALBOX:
mount: mounting LABEL=RECALBOX on /boot_root failed: No such file or directory
Waiting for the root device
Unfortunately, I was not able to capture the logs of initrd...
Feel free to request some more logs if needed.
Thanks in advance!