Here's the real story every time you read about the comparison between multilateral and bilateral international agreements (speaking very generally):
* Powerful nations want bilateral agreements, because it's the strong negotiating with the weak. Imagine the U.S. negotiating a trade deal with Nicaragua: The U.S. position is overwhelmingly strong; they could walk away and cancel all trade with Nicaragua; the U.S. would hardly notice and Nicaragua's economy would be devastated. (EDIT: I'll add that this is true of the powerful everywhere; e.g., large businesses don't want to negotiate with government or Congress (law and regulation) or a class in court (a class action), they want to deal with individual consumers one by one.)
* Supporters of an international rules-based, law-based order, and of a democratic and rights-based order want broad multilateral agreements. Then the weak nations can band together and resist the powerful; it gives them self-determination, the foundation of democracy; it creates rule of law rather than rule of the powerful. Also, instead of an exceptionally complex system of individual agreements between each pair of countries, it creates one standard - much more like a law. Imagine a global business trying to parse the individual trade deals between every pair of countries from its supply chain to its retail customers - an incredibly, needlessly complex level of regulation compared to one international standard. Imagine if the 50 U.S. states only had bilateral trade deals with each other - that would be 1,225 deals, endless red tape for a national business (and there are many more countries than U.S. states). A major reason the U.S. is so wealthy is that it's the largest single, unified economy; that's what the EU hopes to equal.
For example, in the South China Sea, China says they want bilateral negotiations with each country - they oppose the current U.S.-led international order and want negotiations they can dominate. The U.S. and China's neighbors want a multilateral deal; they want to continue the rule of international law and the U.S.-led order, and want to negotiate from a position of strength.
My guess in this case is that it's a reflection of the fact that Trump, the Republicans, and their big business constituents prefer rule of the powerful.