Absolutely Understandable to do that, but there are single tunnels like the Seikan around the world, Not quite as long of course but they run passenger trains there.
Not too much of an inconvenience to get up a couple of hours early and in a couple late for a while to be safe though.
Revenue is the freight train priority reason.
It would seem to me that it would be a massive plus to put a powered switch locations at the end of the tunnels and just run trains through the tunnel that is open on a schedule that would make it feasible to operate and have minimum delays for both...