I think that concern is misplaced.
If you’re currently using MFS 2020, that sim will appreciate all the CPU that you can possibly throw at it. At the moment you will be CPU limited, so moving up to the 9800X3D will likely be a much bigger improvement than changing your graphics card.
To clarify one of the questions in your OP - CPU usage appears to be low - despite the 25 - 35% shown, your CPU is probably at it’s limit.
MSFS 2020 does use multiple CPU cores, though not as well as 2024. The mainthread (core) and one or two other cores will be pretty much flat-out, and several other cores will be getting variable workloads from MFS, but several will be little used or idle.
The percentage readout is reflecting capacity utilisation, rather than outright performance. If 2 cores in an 8 core CPU are being used by a game, and if they are working flat out at maximum speed, then you are at your CPU’s absolute maximum performance limit in that game and it can do no more. The CPU readout in this case will show 25%.
The way to improve CPU performance to noticeable effect in 2020 is either with a lot more speed (intel i9 KS) or with a bit more speed, better workload optimisation and extra 3D cache, like the AMD X3D processors.
Since you already have the 9800X3D, I personally think you will get the best improvement from option D.
If you are already using 4K and performance is currently acceptable, then upgrading GPU first would probably yield little to no improvement. Your current GPU is working hard, but that is to be expected from the 6900XT at 4K.
If the performance limit is with the CPU, then a 7900XTX or RTX 4090 won’t make much of a difference until the CPU can feed them more frames and more detail.