Rework managing hotplug commands with command completions.

Previously the command completion interrupt would post any pending
command immediately before pcib_pcie_hotplug_update() had been
run to inspect the current status. Now, the command completion
interrupt merely clears the flag and stops the timer assuming that
the caller is always going to call pcib_pcie_hotplug_update() to
generate the next hotplug command if one is needed.

While here, fix a bug for systems with command completion where the
old (existing) value was written to the slot control register instead
of the new value. This fixes the complaint about a missing hotplug
interrupt on my T400.

Differential Revision: https://reviews.freebsd.org/D6363