An OS can easily run an app on each for a few milliseconds, look at the performance counters to see which ends up with more instructions executed, and then move the task to where it performs best.
From time to time, it can retry the test, because software frequently changes what it spends time doing.
But apps like factorio are extremely dynamic, so thats either going to be flakey or its going to spend a lot of time/energy bouncing the process between cores.
I wouldn't be too worried about this personally, as configuring the few really sensitive apps with ProcessLasso or Aniancy is pretty easy.
I don't think the average Factorio gamer is going to know that they should do this or how. They will just know that their new CPU which was supposed to have better gaming performance is doing very, very poorly.
I'm pretty sure this is how Nvidia's game ready drivers work. They come with a bunch of pre-made profiles for popular video games, so the optimal settings are configured based on what applications are being executed, which is also why you have to let it scan for your games, so it knows what executables to watch for, so it can properly select the right profile to use.
My understanding is there's a certain amount of nvidia cleaning up after the game developers too. e.g. replacing poor performing shaders with optimised versions or just old-MS style "let's change how the driver works to keep the game working". Which is why they've been so resistant to opening the driver, they believe some of their perf advantage/secret sauce is in the driver rather than the hardware.
Given the primary selling point of these CPUs vs their non-X3D version is having more cache for memory access heavy workloads, if this is not a problem for your workload you're likely not in a position to gain much from the X3D variant anyway.
