I'm talking about this specific bill.

Yeah. Trump was trying to kill that specific bill for weeks. Not just the idea of a border bill - the specific bill that was being negotiated between Republicans and Democrats. He was communicating directly with Senators to get them to stop negotiating, as well as having his proxies and allies send the same message through every channel.

I think Johnson is perfectly capable of looking at a bill on its own merits and saying, "Yup, this sucks, my caucus won't go for it and likely a bunch of border state democrats won't either, so I'll go ahead and declare it DOA" all on his own as was the case here.

It's exceptionally unlikely that he would do the second part. Of course he can look at a bill and figure out whether his caucus will support it or not. But no Speaker is going to get out in front of a major bill like that without first figuring out where Trump is at on the bill.

By the time Johnson made his public statements, Trump had already decided he wanted the bill killed - and let everyone know that. Johnson would not have made those statements about the bill if Trump had wanted it passed - given his tentative elevation to Speaker at that time, he would not have gotten into a direct fight with Trump over policy.