Trk2Rt, optionally, adds route points (shaping points) only from the hidden points (route point extensions in some previously calculated routes) or from track points, if there are any, in the original gpx file. It does not do any routing calculations, so it should never cause any sort of deviation from the original route.
I don't want to speak for
@FrankB, but I can't imagine any way that Trip Manager would cause any deviation form the original route either.
I suspect that the deviations occur on the zumo when it recalculates the route.
Differences in route calculation results can occur between any 2 route planners / navigation devices due to differences in maps, routing algorithms, and user setting for route preferences (e.g. fastest vs shortest) and avoidances (e.g. highways, ferries).
The best way to get the zumo results to match the MRA results is probably to add more points to the route where the deviations occur. Trk2Rt can do that automatically if the original gpx contains a track or route with route point extensions. Otherwise you can do it manually, either in the original route in MRA or later in the process with Trip Manager or on the zumo.
There are tradeoffs to adding points to a route. The more points, the less flexible the route becomes.
Trip Manager does have a helpful route compare capability.
The Trip Manager and Trk2Rt manuals have further discussion of all this, if you are brave enough to read all that very exciting prose
