Its not a bad idea to split up the enclosure like that, in fact most commercial controller does that. You have to think about the in between connectors.3D Printing enclosures is definitely something I'm interested in talking about.
I don't have a printer, but I have a coworker who would be willing to work with me on something like this. He has a couple of printers and likes working on projects like this, so I can make it work.
I figure that I will have to print an enclosure in multiple parts and weld it together due to its size. Another thought I have, that I'd mentioned before, is that I'm considering doing a 2 part enclosure: 1 for the Pi, Power Supply, auxiliary circuitry (5V to 10V converter for the lighting, etc) and a second for the 110v side (connected by a DB15 cable). Anyone have any thoughts on this?
Another thing I'm kicking around in my head is the power supply side. We need 5V for the Pi and other electronics (relays, PCA9685, etc), and 12V for the lighting controller. Has anyone considered just running a 12V supply with a 12v to 5v stepdown converter?
I have thought a lot about the PSU in general. And I would love to recommend/use a single PSU that can feed on AC 110v and gives multiple 5v/12v DC output. There are some readily available buck converters for 12v-> 5v conversion, so If you are only considering that part, just search in amazon and get one of those. I am still in dilemma over whether to just use one or two such converter or use something that includes the 110v AC -> 12v DC conversion as well, that will let me get rid of a all power supply , and just use a single AC supply.