I would have thought the easier way would be a "flags" switch that could do it for you. "flags mainroute". It wouldn't even be an estimate. Maybe some of the Survex folks on this list could shed some light on how feasible that would be. Might require a Survex modification though.
How about as a concept? route <name> <ordered station list> where you can define one or more named routes in the survey network by setting a name then a list of two or more stations that Therion then consecutively finds the cumulative shortest surveyed route between. Maybe it could tack on to the loop detection routine. Therion could then export these as a table in cave-list or survey-list, or it could be its own 'route-list'. Statistics could include total length, altitude gain and loss, altitude range, altitude difference. A debug option could enumerate every survey station along the route Therion has chosen. For visualising would need to highlight the route Therion has chosen in Aven or in Loch. Bruce