flyinmac- I don't doubt your experience and i agree with most of your points. However with my experience:
1) Vertical mounted cards I think is actually a trend that's probably here to stay with PC builds. Many people use riser cables. It's a pretty cool look when done right.
2) I can vouch for the Thermaltake cable. Many of the one star reviews are from the initial revision of the cable which had problems. The latest revision seems to be very rock solid. I have one in my "Mac Pro" PC with an RX580 for several months now. Looks, sounds, and games lovely. The RX580 is also pretty power hungry so if that doesn't cause problems, then it's highly doubtful that a 680 will.
What I find weird though, is you are not really using the cables for looks, but for pure function, and it's probably going to look like a frankenstein computer when you're done. I guess "it will work", maybe it's time to replace the 680s all together? Do you absolutely require a bootscreen, or just think you do? A MacOS + Windows drive needs zero boot screens; pre boot screen drive selector is actually the slowest way to switch between them. But I understand others have many other boot volumes, so yea...
At any rate, I'd consider a GT120 for your boot screens, and move up from the GTX 680. Keplar is long dead. There's still people out there that "think" they need a GTX 680 and will gladly pay for them, so you can recoup some cost.
Here's my PC build using almost entirely spare Mac Pro parts with a 5770 before I put in a RX580. You can see the Thermaltake Riser cable. Really cool build; it's actually faster than my pimped out 5,1 Mac Pro. You can't "feel" any difference between them though, but synthetic benchmarks show otherwise.
W3680 @ 4GHz
12GB DDR3 @ 1600MHz
500GB SSD Windows 10 Pro
RX580
That is a pretty cool looking setup you have there. And I’ll accept and appreciate your experience with it.
In your particular design, if it were me, I’d have gone with a riser card. But I understand if the variables of potential alignments with other chasis designs made it difficult to locate such a card that fit exactly with your intended setup.
Not everyone has access to the equipment necessary to produce their own circuit boards either.
For a hobbiest, there are options to produce one-off circuit boards at home. And I’ve done that as well in some instances where I just needed one, and didn’t desire to get crazy. Such a project can be done in about an hour, aside from the soldering time and time to drill out the holes. Which depending on experience level might take a bit for some people. A dremel works in a pinch.
But I know most are looking for prebuilt solutions.
A riser card / bus provides benefits of reliable long term durability. It won’t degrade, burn up, crosstalk, or act as an antenna for every frequency surrounding you. And it can handle as much power as you can throw at it (naturally within the limits of what you intend to attach to it).
I don’t do circuit design anymore. But I could if the price was right, or if I decided I want to do something custom. I still get the equipment out periodically and build what I want when I either don’t like the available options, or when I want it today and logistics make it impossible for a premade solution to arrive in the next couple of hours.
Had it out yesterday doing some modifications inside a PC. I wanted an internal feature that didn’t exist on the mainboard (PATA) for an old device. So I got out my probes, soldering iron and set to work integrating PATA onto the mainboard. Yeah, I know I could use an external USB adapter, but I didn’t want the drive external.
Yes, I know about PATA to SATA adapters. But I wanted it then and now. Not to wait for shipping.
So, I still dabble as needed. And it’s more fun to get in there and work on the circuit level like I used to. What’s the fun in just plugging things in??
But back to your project, it does look pretty cool. I like it. If I had the extra time, I’d be tempted to get with you and build an expansion bus / riser card combo that would fit it. But it gets hard in these days to find time for projects lol. Looks around the house at all the half done projects... hmmm.... maybe next weekend???

Wait... no next weekend I think there might be something in the lake calling me.
As for your advice to the OP... I concur.