Jason 57

I would also avoid looping cables and passing other cables through that loop.

case setup & power supply mis-match
You can find cables in the lengths you desire, just make sure you get the right cables so you don't smoke the components (good power supplies will refuse to turn on, but you CAN still damage things, and cheap power supplies will just start a fire with the wrong cables attached).
Get some black spray paint and paint the inside of your clear case panel with it, or get a plastic container or small cardboard box and paint it black and stick it over it.  Problem solved.
That looks like a recent model 'Be Quiet' power supply, they're supposedly pretty good, so I would keep the thing if it otherwise works and just change or remove (if not required) offending cables.  Surely you're not the first person with this debacle.
However, avoid any harsh right angles and definitely avoid any 180 degree folds on your cables.  There are metal wires inside that won't bend nearly as many times or as much as the plastic will, and can break.  That can cause all sorts of issues, none of which you want nor should desire to ever have to deal with as they're a real pain-in-the-you-know-where to figure out.  Normal tight routing conditions even after a dozen different times generally won't break anything not defective already, but avoid folding them too tight too many times.

🙁
 

Fractal design 7 xl has 9 pci slots. If that's not enough you can consider server racks. 

the cover is there because they wanted the back of the case flat so less tooling. its a cost saving thing and most case have it.

It's called CHEAP CASE*.  Not knocking your computer at all, but since at-least around 1998~2000 that's been a signature of cheap cases.
When you get your next case, try to avoid any of them with those pesky lock/covers like that, they're just a pain when you can have the simple thumb-screws or other clip-in pressurized (usually plastic) spring or retainer mechanisms.
*Thankfully aside of the 'cheap case' feature, the rest of the case seems very nice by contrast, so surely it's not all bad.
 
Could be worse, it could be a Packard Bell.

Expansion card lock bracket?

Lian Li Lancool II Mesh RGB.
 
I have it. No complaints. Excellent out of the box thermals, too, based on its GN review.  Also relatively easy to work in, though it doesn't have 360mm rad support on the top (only the front) if you care about that.
 
it also comes in a Performance variant with two non-RGB front intake fans if RGB is anathema to you.

You don't necessarily need a different case. Going with something with noise-damping may be more quiet, but you're going to lose a significant amount of cooling potential in the trade. There's nothing about that case that would make it inherently more noisy that anything else, so I would simply just populate it with better fans (which you can then run more slowly, because they're better), and set a silence-optimized fan curve.

Going with RGB is gonna be a mess unless you plan it well, and/or are willing to spend premium. Going cheap usually means lack of features and expanding.

Henlo
 
The Silverstone Sugo SG13 has a lot of volume, while still being really compact (about shoebox sized). It has a full mesh front panel, room for many full ATX sized power supplies, and is recommended with a 120mm intake fan so you get maximum GPU room. If you get a really thick radiator like the Corsair H80i you would be restricted to one fan instead of two but that's not a big deal, I've completed a build with a Ryzen 9 5900X and it worked out pretty well in that configuration.
 
An LED fan looks really nice underneath the mesh. Make sure you avoid the non-mesh version. The V2 is nearly identical to the original, with minor tweaks to the hard drive bracket (which you probably will end up never using)
 
Nothing against the h100, it's a bit large for an ITX case though. Like the h510 from Nzxt, it's sort of in a "baby ATX" category, a little closer to your average micro ATX case.

Plenty. I've got a 280mm rad up top with 2x140mm fans attached. You'll have no issue at all just fitting the fans.

you can always make extra holes
 

1. get a case with front mesh for better airflow.
2. 5950x if you need a CPU for that workload.
3. 3600mhz ram
4. swap it for a 3090 if you can the VRAM may actually be useful for you.
5. go x570
6. 850w is likely enough do go any lower.
7. use pcie 4.0 drives. WD SN850 would be my recommendation. 
8. use more ssd storage, avoid hdd.
9. not required use onboard (if thats what you mean then ok)

You are overpaying for those samsung ssds, consider getting a different brand

well just mount the rad and fans on the outside vs the inside if you need room

Lian Li 205M. 
 
Cooler Master MB311L.
 
You don't need a wind tunnel for a 3600 and a 2060. 

My new case (Lancool 2 Mesh), I wipe off the front and top when I see dust build up. 
We have 8 cats and No carpet. 
When I install my CPU cooler and case fans, hopefully a NVMe drive as well soon, I plan to wipe down the interior. 
At least I don't put the case on the floor anymore. 
 

Unfortunately I need to disassemble it anyway to replace the HDD, but luckily found that there are only 2 plastic clips.

They look good in the everybuild I see 

I'll occasionally wipe down the dust filters, but my desktop really only gets a full cleaning whenever I do a hardware upgrade. It doesn't get dusty enough to warrant going out of my way to open it up and clean it.

Not nearly often enough.

Good news, they actually sent a new kit and working just fine, but im actually un-becoming a Lian Li supporter for another reasons

freeagent

This ain't your daddies WD40...

 

Clean it with alcohol and a q-tip and maybe spray some wd 40 into the fan bearings, then clean it again. Let it dry completely before using again