isci: Move transport layer registers from port to phy

At init and RNC resume we need to touch every phy in a port to be sure
we have initialized STP properties in the case where port_index !=
phy_index.  Also add some missing __iomem annotations.

Signed-off-by: Henryk Dembkowski <henryk.dembkowski@intel.com>
Signed-off-by: Dan Williams <dan.j.williams@intel.com>