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The IO range space is pretty limited and each PCIe port is actually a PCI bridge consuming 4K IO range even if devices behind it are PCIe and do not require IO Ports at all.

QEMU's Generic PCIe Root Port has a new property called io-reserve and setting it to 0 does the trick:
   -device pice-root-port,io-reserve=0

Libvirt should set io-reserve=0 by default for all ports expect ports used or planned to be used with the new pcie-pci bridge that allows using PCI devices on a PCIe machine.

Libvirt can't just add  io-reserve=0 onto ports by default at this point, because it would be a machine ABI change that would break migration compatibility for all previously deployed guests.

(In reply to Daniel Berrange from comment #2)
> Libvirt can't just add  io-reserve=0 onto ports by default at this point,
> because it would be a machine ABI change that would break migration
> compatibility for all previously deployed guests.

What about for all the new xml domains?

I believe this is a dup of bug 1408810. Please reopen this one if I am mistaken. Thanks.

*** This bug has been marked as a duplicate of bug 1408810 ***