Poor thermals, some laptops are designed to work with thermal throthling, I was repasting friends MSI laptop, and I gained from 30 seconds that was throttling to 60 seconds before it started throttling, using prime 95 to stress test it.
Ok, about heat sink it has thermal pad? And you removed the plastic cover for thermal pad?
About load, do You have windows 10, and it is not doing any background tasks, and if antivirus software is not working on the background?
And can you check other components temperatures? On for example hw...
Have You checked power and extension cords?
I hope it would not happen again, but if you can try to check if you can spot the difference in temperature of power cords, cause where is burned smell there is higher load, and more heat from cables.
About 3.5 HDD, I hate them to have in my case, cause they are so laud I will try to buy one of those https://www.orico.shop/en/orico-transparent-docking-station-for-25-or-35-inc.html
Cause i only need hdd for 5 minutes per day to work to make backup and then power them off.
About motherboard, check if seller is giving updated bios cause this board was meant to use ryzen 2000 series, and with new bios it will work with ryzen 3000 series.
And this motherboard has to low bios memory to support full MSI bios and You will get gse light version...
The sx 8800 is one sided ssd, so the memory chips are stored on one side of ssd.
They say on it's website that is intended to use in laptops.
Sx 8100 I think is double sided ssd, but after work I will search more.
I like the idea of mobo rotated 90 degrees, my work program uses hardware USB key, and it works good only in back USB, so I've got case on my desk and back on front. So that layout could help me get the case under the desk again.
It's a shame that did not work for you, some ppl in Internet says it's due to the exceed of the power that battery /wall charger can input to parts. Can you try to play pes 2019 with max procesor state on 90% and check temperatures? If this won't work I don't know what could help you, sorry.