How can the user set a false path on my pre-synthesis constraint files (SDC/FDC) between the PLL clock outputs if these are generated in the post-synthesis stage?
To set this as false_path in pre-synthesis, user need to define the create_generated_clock on the SDC/FDC file as well. Just make sure that the create_generated_clock constraint at the pre-synthesis stage captures all of the properties of the PLL clock output (i.e. frequency, phase, etc.).
Since this is a user-defined constraint, this would be propagated throughout the compilation process and override any automatic definitions by the tool (which is the automatic definition done in the post-synthesis stage).
Once the user have defined their create_generated_clock constraints in the FDC file, you can now define a set_false_path with these generated clocks.