x86/amd-iommu: Set iommu configuration flags in enable-loop

This patch moves the setting of the configuration and
feature flags out out the acpi table parsing path and moves
it into the iommu-enable path. This is needed to reliably
fix resume-from-s3.

Cc: stable@kernel.org
Signed-off-by: Joerg Roedel <joerg.roedel@amd.com>