I'm going to be hand wiring
one of these entirely custom beauties fairly soon.

Not mine! But Matteo's cutting metal for me, too. One layer for the plate — naturally you have to plate mount when there is no PCB — and a handful more for the case.
The wiring goes something like this:

Diodes all the way down.
Cherry MX switches have space for an LED to snuggle in with them, so you get natural backlight capability with them anyway. While I'm putting this keyboard together I'll get a good idea of what changes, if any, are required to hook up a whole separate matrix for lights, too. I doubt I can do it with my first, but custom keyboards are addictive and it could well be in my second.
A separate matrix for lighting means I can address every LED individually from the controller. So you can expect individual "cooling" like it sounds the Ducky Shine 3 does. All without bothering the host computer, or needing drivers. I'm thinking of a heat map mode where each key shines when pressed, but fades to a gentle background state dependent on how much use it's getting. Playing games would slowly light up your movement cluster, for instance, while writing like I do would get backspace glowing pretty nicely!
One actually useful lighting mode would be to highlight the arrow keys on my 60%'s layers. I'm going for ESDF but might want to switch to IJKL or what have you. Lights can really assist function-layer-crazy memory.
Anyway, I'll look into it.