For some years, railroads, and trains, tickets through New York and/or Washington (and maybe other stations where many trains terminated) on through trains were priced higher than the sum of the local fares, possibly so those through passengers could make a lower density coach pay its way.
First, concur with Mr. Boylan that an interline fare, say, Boston to Philadelphia marked Via Hell Gate Bridge was greater than the two Local fares, which one first rode to GCT, thence transferred to Penn.
An "old New Haven hand" once referred that to me as "bridge toll".