Thanks to @kevans91 for pointing me in the right direction. FreeBSD had the same bug as Linux (see https://bugzilla.kernel.org/show_bug.cgi?id=217276) where the ultimate solution was to honor the brcm,enable-l1ss FDT property.

In current versions of the dtb files this property has been added by default.

Without this on many, many pcie addin cards the pcib will Serror when trying to assert the clreq# pin on the pcie bus. Many cards do not have these hooked up.

I have done the following

1. Without the patch applied, attach non-RPI specific PCIe devices to the PCIe bus. Observe the Serror
2. Apply the patch, observe that the Serror goes away, and the PCIe device works