We ended up with two versions of the GPX file, which only differ at the final Table Track section of the route. One version takes Table Track from the Avonbeg river bridge down to Baravore, while the second version follows the longer road between those points. On the night of the race, we basically chose the shorter Table Track option, but I'm not convinced it was faster. Near the end of a long overnight race, I think the road is a safer bet.
I had issues with both GPS recordings of my run - my own watch lost everything up to CP2 due to some kind of glitch, and the Primal tracker (issued by the race organisers) seems to have stopped recording somewhere on Table Track. However, GOT's recording should be a fairly accurate approximation to my own run since we were together the whole way.