Did you already try with this and got the same result or you are saying it without trying it?
We have integrated latest DesignWare code from Kernel-4.14 to Kernel-4.9 and as part of that looks like there are some things outside of DesignWare code missed out in the integration.
Just to give some background about how the interrupt number gets updated in the configuration space,
in TX1/TX2, it is done through the call
pci_fixup_irqs(pci_common_swizzle, tegra_pcie_map_irq);
but, in DesignWare core, ‘pci_common_swizzle’ and ‘of_irq_parse_and_map_pci’ are registered with the host bridge hooks and they are used in pci_assign_irq() API in setup-irq.c file.
In Kernel-4.14, pci_assign_irq() is called explicitly in pci_device_probe() API in pci-driver.c file whereas the same thing got missed out during integration. Hence, I asked you to add that and check.