A wild Saber appears! (depending on how fanatical you about the F/sn VN, you may actually recognize my username or its abbreviated form "NM64")
Anyway, I hope you're OK with the fact that I used one of your photos in order to prove a point that, with a properly-designed micro ATX motherboard and a 2-slot GPU in an micro ATX case, you'll be left with two empty slots rather than just one between the bottom of the GPU and the PSU:
Regarding chipset temps, you could always split the difference and use a graphite pad instead which is supposed to be comparable to something like stock thermal paste when fresh (though a pad has the obvious benefit of never degrading) - both Innovation Cooling and Thermal Grizzly make such a product (Innovation Cooling's is more foil-like while Thermal Grizzly's is more cloth-like).
You'd just have to keep in mind that graphite may need a decent amount of pressure (which I'm not sure the chipset heatsink can provide enough of - you may want to check before hand).
Also graphite is electrically conductive, so you'd want to cut it down to the necessary chipset die size and probably should insulate the area around the die with electrical tape just to make sure everything stays safe.
But graphite pads are also kind of slippery, and that combined with possibly minimal heatsink mounting pressure might actually mean it'd be better to cut the graphite pad to be considerably wider than necessasy so that it hangs off on the sides of the chipset die (with electrical tape under the graphite to insulate things of course), and then tape those hanging-off edges of the graphite onto the electrical tape you put onto the board itself so that everything is held in place
Protip: regarding the "AMD" ring on the stock CPU fan, it can be removed and rotated so that it's not blocking your RAM.
In fact, removing it is required to even fit the fan into some really small form factor cases (this is most notable with the Wraith Stealth and the ASRock DeskMini A300).
I'll go watercooling next.
I'll go watercooling next.
Uhhh, I would really advise against that since the motherboard you chose has quite toasty VRMs, so sticking with a down-firing CPU cooler will help keep said VRMs cool, even more-so since you also bought a case with relatively poor cooling capability.
(spoiler: the one motherboard that's alluded to as being sucky is the very same MSI board that you bought)
.....though at least you're only running a 3600 so your power-draw and therefore VRM temps should remain low even on the crappiest of AM4 motherboards; just be wary if you decide to upgrade your CPU to something higher-end.
The CPU fan shroud with the "AMD" logo can be rotated and/or flat out removed without needed to also remove the heatsink from the CPU itself.
This trick to remove the shroud is in fact what people do to fit the wraith stealth cooler into the ASRock DeskMini (which it too short with the shroud, but without the shroud it just fits).
Regarding the H500, one of the things is that it seems to have increased in price recently, so at its current price-point it's up against much better cases like the Fractal Design Meshify C.
To put the H500's price into perspective, the Cooler Master NR600 with a stock fan config performs extremely similarly to the H500 also with a stock fan config, yet the NR600 is $20 cheaper and is not only arguably a more practical case as well but the NR600's cooling performance scales much better with additional fans than if you were to add the very same fans in the exact same configuration to the H500.
I just realized - you've got a full-on custom watercooled CPU and GPU, yet are still using the motherboard's dinky chipset fan...
...then again, apparently the Aorus Xtreme wasn't available at launch, and I'm guessing even the Asrock Aqua is a bit out of your price range?
...stability issues at stock clocks? O_o Seems odd considering Hardware Unboxed just posted a video demonstrating a 3900X running on a lowly ASRock B350M Pro4, and you have a full-on X370 Taichi with a lower-end 3700X.
Steve did however mention that he could only hit DDR4-3000 with a Ryzen 3600 on the B350 board even though the 3900X managed 3200 on the same board, and that running at DDR4-3200 with the R5 3600 would result in BSODs and such.
Therefore I don't suppose the stability issues would go away with the CPU at stock clocks if you simply reduce your RAM speeds?
But that's just the stock clocks which itself may be due to power and/or heat rather than anything architecturally, and you have full-on custom water cooling.
I mean, it's been shown that Ryzen's limitation with clockspeed is looking to just be a yields thing as a 3900X is overclocking better than a 3600 non-X, so one would expect a 3950X to be binned even better. Additionally a 3950X, being two 8core chiplets, is kind of nothing more than two 3700X or 3800X (one 8core chiplet) on a single PCB, so again outside of heat and power there shouldn't really be anything stopping you from hitting similar all-core overclocks (unless you lose the silicon lottery).
Why lock the 3700X to its base 3.6GHz and effectively disable turbo?
Now you have an excuse to hop onto the 3950X when it's released.
Some high-end Asus boards have it as well; also note that not all MSI boards have it (for whatever reason it's more common on their B450 boards than X470).
There's a list of motherboards that have this feature over on /r/AMD:
Of course, but my idea was to use a 2200G by itself or a 2400G by itself for a price similar to an Athlon + GT 1030 combo.
The only way I can see Athlon + GT 1030 combo being the wiser choice is if you already have the GT 1030 or you absolutely need some sort of functionality that an Nvidia GPU provides that an AMD GPU does not.
Reference pricing taken from ca.pcpartpicker.com:
$73 CAD - Athlon 200GE
$109 CAD - cheapest GT 1030 GGDR5
$123 CAD - Ryzen 2200G
$189 CAD - Ryzen 2400G
Indeed was, past-tense.
Gigabyte has since gotten the the same memo as MSI and has hopped on the 200GE-overclocking bandwagon:
Well once grandma is ready to get her game on, make sure to update the motherboard BIOS so she can overclock her shiny new Athlon to 3.8+GHz as well! (Gigabyte very recently implemented support for this)
Actually there's a few reports around that Gigabyte got MSI's memo and has VERY recently (like the last couple days) implemented overclocking support for the Athlon 200GE as well:
Video demonstration (not my video): https://youtu.be/OJaKeUKKN08
It is worth nothing that the crimped type of molex-sata adapters seem to be perfectly safe...though the adapter in question clearly is of the molded type which matches the kind that can in fact catch fire due to shorting out.
(also for reference, the few images floating around the internet depicting burnt crimped sata connectors are actually connectors from power supplies themselves - the key identifier is the orange 3.3v wire which is present on PSUs but not on molex-sata adapters)
For a similar if not cheaper price for way better CPU performance, you'd be better off going with a Ryzen 2200G or Ryzen 2400G and just using the integrated graphics by itself instead (which performs similarly to the GT 1030 GDDR5 and absolutely obliterates the GT 1030 DDR4).