I had a post in Chinese but maybe this helps more people who wants to simulate the tolerance of their systems using ZPL.

 如何使用ZPL改变POP中的beam和fiber数据 | Zemax Community

The MODIFYSETTING can be applied on the .CFG which has the same name of your design file and locates 
under the same directory of your file. This is the file that the POPD reads. You have to manually click the SAVE button to generate this file first. If we modify the POP.CFG, it does not work.
Here is the sample ZPL code.

popCFG$ = "C:\Users\Desktop\Fiber Coupling.CFG"
MODIFYSETTINGS popCFG$, POP_FPARAM1, 0.005
MODIFYSETTINGS popCFG$, POP_FPARAM2, 0.005
OPENANALYSISWINDOW POP, popCFG$
PRINT MFCN()

The OPENANALYSISWINDOW may not be necessary for certain users. When I run the test, I need this line to activate the modification on this CFG file.