How can I configure more detailed settings for NativeLink using VCS or VCSMX?

I see, from the information I have currently, this option should not affect your simulation.

When using vcs, we usually use the script generated by quartus and should add custom options to it manually.

You can check the following information first: https://www.intel.com/content/www/us/en/docs/programmable/683102/23-1/sourcing-synopsys-vcs-simulator-setup.html

And the following AXI simulation flow (page 686 Synopsys VCS Simulation)may also be helpful:

https://www.intel.com/content/www/us/en/content-details/820953/mentor-vip-intel-fpga-edition-amba-axi3-and-axi4-user-guide.html

I'm also investigating on this, if any question please let me know.