First of all, the hardware part, yes. There is no difference. However, there are cases and versions that require a 5800X3D-compatible UEFI update. Each company has released a version, so you may need to check and work with them.(Maybe need AGESA Combo V2 PI 1.2.0.7)
In my experience and subjective opinion, there is probably no case where the 5800X3D underperforms the 5950X in MSFS play.
The heavy load region (0-1000ft) is where the scores are closest on both CPUs, and this region depends on the raw speed and latency of memory, memory controller and IOD traffic.
(Even so, X3D is probably 10-15% faster).
In the heavy load region, even if there are cores, they will be waiting for data from memory and will not be able to turn around the process.
If you want to describe it, you can describe it as “limited by CPU uncores”, similar to the “limited by main threads” we often see in MSFS.
X3D is by far the better choice for both medium (1000-5000ft) and light (5000ft-) loads. (+30-40%)
This is because data is fed more frequently at higher speeds.
It also has an advantage in stutters. This is because cache miss-hits are reduced.
Hence the advantage in VR as well. in VR I believe there are X3D results in various threads, but I think it’s the same trend in the right direction.
As you point out, I think the difference in workloads other than MSFS will be the main factor.
For example, if you are doing OBS CPU encoded streams (image quality oriented), there may be a pattern where the 5950X may have an advantage when properly processor affinity is used, etc.