I feel like I'm way out of my depth giving you advice 
this is a build for big boys. I haven't done a custom loop yet, hopefully this Christmas holiday, I'm waiting on my parts. But I did a lot of research (I think about two weeks and over 30 hours) ending up with this part list.
Your cable management challenges alone are nightmare inducing , but it's going to be so satisfying to get this right. If this were my build I would probably try and measure each power and data cable and order them in custom length/color/sleeving to make it absolutely perfect.
The fan cable management is going to be a nightmare with PWM+RGB. You could consider the Lian Li UNI fan system which allows you to daisy chain them to a maximum of 4 leaving only a two cables for PWM+RGB. I wonder if that can integrate into the iCUE system or Aquacomputer stuff.
Do you have temperature sensor(s) in your loop to control the fan speed based on the coolant temperature? That's my plan at least, I do it now also with my Corsair AIO cooler. Both iCUE and Aquasuite can do this. I have no experience with Aqausuite but I've watched a couple of YouTube videos and it looks like good software.
For aesthetic reasons I probably wouldn't want to have Quick Disconnect fittings. I think this is more appropriate in a Test Bench situation but not for a production build. What kind of tubing do you have now, soft or hard?
With such a big case and the fact that you have two RTX 3090s (lucky guy ) I would probably do two separate loops. I would run the CPU loop of a single 480mm radiator and then run the two GPUs through the other 480mm and 360mm.
By default you can run 6 fans from a single Commander Pro for PWM. I'm planning on doing 9 with 2-way splitters but the 3 extra will have PWM only no RGB. This should be doable but there is a limit to what kind of power you can draw from a single Commander Pro. I've read that 3-way splitters do not work and can break your Commander Pro.
The LL120 3-pack comes with a RGB hub and a Lighting Node PRO. The RGB hub can control the RGB for 6 fans also. There are multiple ways to do this I think. You could use 3 Commander Pros and 3 RGB hubs, this will give you exactly 18 PWM+RGB headers. Then you could use the Lighting Node PROs that come with the LL120 3-pack also to connect other D-RGB stuff like RGB water blocks if you have them. But you would need the adapter cables I mentioned in my previous post.
Other options are maybe using generic D-RGB hubs or controllers. You need to keep in mind that there is a limit to the amount of D-RGB LEDs you can run on a single connector. Each LL120 fan has 16 LEDs and the QL120 have 34(!). I believe the maximum amount of LEDs you can rung through a single Lighting channel on the Commander Pro or Lighting Node PRO is 60.
This is a build that needs a lot of planning for RGB and also the PWM control if you want a perfect silent system. Not even mentioning if you have any kind of "theme" in mind in terms of color.
And yes, you definitely want to have a drain installed for both loops in the future for maintenance.
