Yes, TPE run loads of trains over unusual routes (either unusual to any passenger trains or merely unusual to TPE) in order to retain route knowledge over a wide variety of diversionary routes.
Taken to an extreme, a York-Liverpool train can be off the usual route for the entire journey with the exception of the York-Church Fenton, and the short section between the junctions either side of Mirfield (Thornhill Junction and Heaton Lodge East Junction), plus Edge Hill to Liverpool, so that's less than 15 miles that can't be diverted, all the rest can!