From all the stuff I've read about 19th century railroad building, it wasn't the B&M that wanted to route passengers via Troy, it was the Trojans that wanted to route traffic eastward to Boston, bypassing Albany. It was Troy that drove construction of the Troy and Boston Railroad eastward to take advantage of the Hoosac Tunnel. At that time, Troy and Albany were seriously competitive. A second factor would have been the Vanderbilt family's determination to prevent the B&M from entering Albany and competing with the Boston and Albany line of their New York Central. The whole story has been the subject of several books, but this is the condensed version.
PBM