Everyone--well, almost everyone--understands that the power of any majority in Congress is limited. Even if a majority wants to get something done, it might not be able to accomplish that due to our system of checks and balances. Thus, one can understand why Republicans might relent on defunding a program that is one of the President Obama's top priorities because defunding that program might lead to a round of budgetary brinkmanship.
But the omnibus's quadrupling of the H-2B visa program is not because of limits on Congressional Republicans' power--it's a policy that they have used their power to realize. It's not like Barack Obama would have vetoed the omnibus had it not included the H-2B expansion. Congressional Democrats would not have shut down the omnibus over a lack of H-2Bs. No, as Conn Carroll, Mike Lee's communications director, put it, the H-2B expansion is a "'Republican' ask." Republican leadership chose to make expanding the H-2B a priority--when they did not make priorities out of reforms to refugee programs, funding of the border fence, or cracking down on "sanctuary" cities.
From a Republican point of view, expanding the H-2B program makes little political sense. Republicans face a grassroots rebellion, and they also need to do more to reach out to the economic middle. The H-2B expansion inflames this rebellion, and it further undermines the working class; it also runs contrary to the principles of the free market. Embracing a pro-opportunity conservatism seems a better route to a majority coalition than being the party of K Street.