IMO, if someone hasn't shown up by the time boarding has completed (unlikely a connecting pax at 6am) then they clearly didn't make it to the airport on time. I find it hard to believe that they were at the airport for the 60 min cut-off, but if customs is routinely taking longer than 45 mins for pax to clear, then perhaps the check-in cut-off needs to be amended to 75-90 mins. I don't agree with waiting, I also think the policy of having to remove bags should be revisited (recognize that is likely a government regulatory rule) as I agree that is routinely an issue.