I won't use the backplane. The main issue is that the RAID controller is located there and not on the original motherboard, and I can't interact with it (physically difficult, and, ironically enough, it's an Armada chip with very poor documentation preventing me from running FreeNAS on the thing in the first place). I'll just go with cables as-is for now, and if ever, I'll try to make a custom PCB with just passthrough Power / SATA.
I do want to use the existing status LEDs though, at least. The rest of my plans would be to use the buttons as well (interfacing them with GPIO, but not sure what scenarios I want to have here), re-route the front USB, and maybe have another identical 1.3" OLED screen on the I²C bus to "fill" the Qnap front display cutout. No idea how feasible all of this is; it should all fit, but cable management is likely to be very tricky.