BUT you "don't have to do that" if you don't want to.
As noted you can pick up the "Erie Canal Towpath" from the Peace Bridge in Buffalo and stay in the US the entire time. ( not well marked at the onset but with a bit of study you can get through the initial confusion. I have the Buffalo to Tonawanda route info if you need it)
And in Montana at Glacier NP there is a non-Canada option "Marias Alternate". My 2008 copy of the NT shows that option. You can avoid Canada if you desire and still be following NT maps.
Sorry for adding to your confusion. I used the ACA Erie Connector route through Michigan and Canada to the Peace Bridge and then was back on ACA NT for NY. Many ways to do it as you will learn from the ACA folks.