Since you like the bike otherwise, just decide if you think the Praxis crank in it of a comparable tier level to the Ultegra crank. You might find the spec's on the website for that specific model of Domane and if it's not a Praxis crank then use that maybe to see if you can get a better deal. Though likely not unless you are a good at this type of negotiation.
The specs on the model I saw did show a Ultegra FC-R8000 crank with a Praxis T47 BB compatible with Shimano Hollowtech II crank spindle sizes. Maybe the Trek Dealer can show you the specs for that particular model you looked at which might indeed be different. It's not too uncommon for lower tier models of the same frame bike to have mixed components.