PCI/VFIO: use pcie_flags_reg instead of access PCI-E Capabilities Register

Currently, we use pcie_flags_reg to cache PCI-E Capabilities Register,
because PCI-E Capabilities Register bits are almost read-only. This patch
use pcie_caps_reg() instead of another access PCI-E Capabilities Register.

Signed-off-by: Yijing Wang <wangyijing@huawei.com>
Signed-off-by: Alex Williamson <alex.williamson@redhat.com>