The Border Patrol shouldn't be boarding Amtrak trains looking for anything other than illegals. If they happen to catch an illegal alien who is also smuggling drugs, well so be it. But they shouldn't be looking for that except at an actual border crossing.
While I'm hardly an expert in this area, I am a frequent traveler across the US/CANADIAN border.
It's been my opinion that the US Customs & Immigration is charged with both looking out for illegal aliens AND looking out for smuggling, in addition to other stuff. We were once pulled into secondary in Port Huron, MI, where an un-eaten half of a sub sandwich was confiscated because of the "no beef from Canada" law. My wife offered to produce the eaten half of the sub, but they declined.
I think that the border patrol can board an Amtrak train (within that 100 mile limit) in order to enforce immigration laws, and also contraband laws, like Cuban cigars, if they have reason to suspect.
While time consuming, random checks are not unusual at automobile crossings.
And remember just 10 years ago there were talks going on with the US and Canada to just open the borders, and do away with the checks? 9/11 sure changed things.