I want to highly recommend installing the beta BIOS, because the AGESA 1.2.0.6c is a very important microcode update for the CPU, direct from AMD. The AGESA 1.2.0.5 microcode (or what MSI call "AMD ComboAm4v2PI") used in the previous BIOS vHD is problematic, see
here. Don't let the "beta" tag unsettle you, it's just because they wanted to get this out as soon as possible. Other brands also released it as a beta, i think.
Ok, going through your screenshots. Your power draw in idle and under load is ever so slightly elevated, normally i'd like to see about 10W less each for a 3900X, maybe that's something that the new AGESA can also tackle (it's like a code update for the CPU, they can modify all kinds of parameters). Still, it's a bit of a mistery why the Wraith Prism should underperform that much. It should be able to keep this under 90°C.
So if you think the pre-applied TIM wasn't good or not enough, then cleaning it properly (i use Isopropanol) and applying better thermal paste might be worth a try. It's also possible that you need to tweak your case fan curves a bit to help the CPU cooler along, see my thread,
Guide: How to set up a fan curve in the BIOS
If this doesn't help, look at an aftermarket tower cooler like a be quiet! Shadow Rock Slim 2 (
review) for example.
Oh, another thing i noticed: You are running your RAM at the safe JEDEC profile of DDR4-2133, leaving lots of performance on the table and bottlenecking the CPU. You should (now or after the BIOS update you will hopefully do) enter the BIOS and enable A-XMP for the proper RAM speed.