Good, or bad, now it's at least known that something excact is clearly something it shouldn't.
Is it a cause is another thing.
I don't know the correct PCI naming policies and the whole PCI hierarchy has always been a bit messy.
A controller can also be PCI to PCI and then another PCI controller is what you think is the first one.
Did I read it right that this 440EP can also be a PCI controller, so the 2nd in PCI line.
One construction model is CPU-PLB-bridge-PCI-controller/bridge-stuff.
There is also a method called PCI boot, where PCI memory can be accessed without configuration, it can obviously be misused for what ever purposes.
In this case it's quite possible that PCI something is predefined.
Since the system knows that some parts are there, or should be, always, it can expect them.
So if PCI 9056 is not first its missing ID request can be fine, but since that other boot log has it as first, one must follow that.
Though it doesn't exclude that there isn't something else before that but would it be completely silent in the log.
For the interrupt,
if it's PCI and not configured it should be ingnored.
One method for IDSEL is to decode one address line for each PCI connection IDSEL.
PPC440EPx-GRx manual says that device 1 is AD11.
If those addresses are used elsewhere there must be a chip with enable in between somewhere.