Interesting, we’re same same in case and cutting the Sata part 
You’re is very clean as you put it all in the Nas case but for it that case’s shipping is more expensive than the case itself in my region. I will soon start working on making a custom case for my current NAS
BTW I forgot to remove the protective sticker or maybe I did that on purpose, I don’t remember. But without the sticker it looks so cool.
I have root / on ssd while /boot on sdcard or emmc.
You can try to flash uboot on emmc/sdcard and flash os on sata ssd and it should boot from ssd given that uboot have pcie support.
Then you can flash uboot on sd/emmc along with /boot partition so the initramfs will load from it and then hand over control to linux kernel which will mount /root on ssd and start the os. I am following this approach on my nas.
