Have their shit together meaning they can actually function as a coherent group to achieve actually getting something done, whether I agree with them or not. When you toss the “Freedom Caucus” into the fray and if you refuse to work at all with democrats, then the party “does not have their shit together” insofar as they can’t pass anything. To try to pick their own speaker they utterly struggled.
Here they wanted the government to keep functioning by and large, but a small contingent just wants to burn everything down. The fact that the larger population of GOP were willing to work with Democrats rather than try to appease the nutjob wing is evidence that they “have their shit together” enough to actually get something passed they wanted to get passed.