TLDR at bottom.
The mainboard USB4 should be able to handle all of that.
The big difference is that the port on the graphics module is connected to the dGPU (the dedicated GPU in the graphics module) whereas the ports on the mainboard are connected to the iGPU (the GPU integrated into the CPU).
When using the graphics module and using a port on the mainboard the dGPU will still do most of the work, however the iGPU will handle the final outputting to the display.
The iGPU does support outputting at up to 8k 60Hz or 4k 240Hz and up to 4 displays and freesync, so the mainboard ports should be plenty capable of driving displays. However the additional step of having the iGPU do the outputting does result in a slight performance penalty, which is why the graphics module does have a port.
The USB-C ports on the mainboard should be fully capable of running all that you want, however with an ~10% performance penalty due to the iGPU handling the final outputting to the display.
The USB-C port in the graphics module on the other hand should get full display performance, however is severely limited in other capabilities. The port has 480 Mbps of other bandwidth (for purposes other than displays) and it has not been announced if it will support charging through that port (I doubt it will).
Although that last part (charging support) may not matter much because afaik there are not yet any docks that support the new charging standard that Framework is using, so for now using it in a dock would limit the charging speed (and you could even lose charge while using it and docked). So I personally would suggest using a separate cable for charging anyway.
So what you could do is use the graphics module’s port for displays and peripherals (the limited bandwidth for non-display purposes is still plenty for basic peripherals and even is double the speed of the average internet connection so it can be useful for ethernet as well) and use a port on the laptop for charging.
Although beware that many docks attempt to reallocate half of the bandwidth away from displays and too USB instead, however since the graphics module does not support that the bandwidth is just wasted (which can result in displays being limited to lower settings due to inadequate bandwidth). So if you do want to use the port on the graphics module I suggest this dual display or this single display dock from Cable Matters as those allow full bandwidth to the display.
Mainboard ports have an ~10% reduction in graphics module performance.
Graphics module ports have reduced bandwidth for purposes other than displays and it is unknown if charging will be supported (I doubt it).
So to get full capabilities a two cable solution will be needed, although even if there weren’t those limitations it would likely still be beneficial anyway due to the lack of docking stations currently available with support for the full charging power of the Framework 16.