In the short term, no-one can predict what will happen in the event of an unexpected imposition of border checks without time for proper preparation.
However, I think in the long term, if full customs checks become a permanent reality, it could definitely be an advantage for rail, which due it's predictable nature, scheduling and the small number of operators with direct interaction with the border agencies, will be able to arrange the necessary customs resources in advance and offer dependable services, unlike road hauliers. If you look at other external EU borders like Poland <-> Ukraine or Romania <-> Moldova, the rail traffic runs smoother than the road traffic.
I was talking to a Ukrainian woman recently who told me she always prefers to take the train when going to Poland, even though she was a student with not much cash, because the queues at the border for road vehicles are between 3 and 12 hours depending on the how thoroughly the border checks are being conducted, but for rail movements the checks happen immediately. Admittedly this is for passenger not for freight, but it demonstrates the concept.