Only reason I’d get the Checkpoint over the Domane, in your situation, is if I wanted to run 42mm or wider tires. The Domane comes with 32 mm, is officially rated by Trek to accept 38mm tires, and will easily hold a 40mm tire.
I’ve extensively test ridden the Domane as well as many of the comparable bikes from other manufacturers, and the Domane is pretty impressive for an endurance bike. I plan to add one to my stable in the near future, SL5.
And I don’t understand why the Trek paint is supposedly so fragile on the Domane for gravel. If that’s a concern, just install some clear bra on the bottom part of the downtube.