thunderbolt: Set port configured for both ends of the link

Both ends of the link needs to have this set. Otherwise the link is not
re-established properly after sleep. Now since it is possible to have
mixed USB4 and Thunderbolt 1, 2 and 3 devices we need to split the link
configuration functionality to happen per port so we can pick the
correct implementation.

Signed-off-by: Mika Westerberg <mika.westerberg@linux.intel.com>