"So I'm wondering whether to modify the order in Eclipse or disable the Checkstyle check. Leaning towards disabling the Checkstyle check so everyone who joins the project doesn't have to modify their Eclipse settings but it seems a bit wrong to be ignoring the official conventions."
I would suggest changing Eclipse to conform to the rules that YOU want to use. Preferably using Oracles if that what you want. I usually generate my Eclipse project files using Maven (so all code formatting is created automatically for new users). I know CXF uses something similar, take a look at their POMs for inspiration.