No, the reference design in AN708 Application Note is for hardware functional test only, not for simulation.
You may see one of the following errors:
INFO: 175149 ns RP LTSSM State: DETECT.ACTIVE
FATAL: 175149 ns LTSSM does not change from DETECT.QUIET
FAILURE: Simulation stopped due to Fatal error!
FAILURE: Simulation stopped due to error!
$finish called from file "./../..//../../ip/top_tb/top_tb_DUT_pcie_tb/altera_pcie_a10_tbed_161/sim/altpcietb_ltssm_mon.v", line 155.
To run the Intel® Arria® 10 PCI Express simulation, generate the testbench by following the steps provided in Chapter 2 of " Intel® Arria® 10 or Intel® Cyclone® 10 GX Avalon® Memory-Mapped (Avalon-MM) DMA Interface for PCI Express* Solutions User Guide".