Boeing is protesting a standard industry practice to basically stop the sale of a type of jet they don't make, for an order they wouldn't get. And it's likely to potentially cost them UK/CA government business.
Is Boeing doing this to really prevent the maybe someday still entirely hypothetical C-500 which even if they started today is minimum 5 years away and might compete with the smaller 737's?
This leads me to believe one of three things is happening:
1) they wanted to file the protest on the C100's to ensure they're on record when/if a C500 ever does happen and they fully expected this case to get thrown out, but they underestimated the protectionism of the current administration.
2) Boeing is being leaned on by someone in the administration to file this as a bargaining chip for further NAFTA negotiations.
3) Some in the administration are super jealous of Justin Trudeau's hair, and are hoping that blocking the deal with muss it all up.