I see your tour does the Flam to Gudvangen cruise, and then the Gudvangen to Voss road journey (having arrived in Flam by road) so there is really no need to repeat those.
The Bergen to Flam express boat only repeats about an hour of the Gudvangen to Flam cruise, so compared to what else you see on the Bergen to Flam express boat that isn't an obvious problem.
I saw a You Tube video this week from a Texan blogger (and whose work is always excellent) who had done the NiN route but with two self booked deviations- one from Aurland (having stayed there in preference to Flam) to Laerdal (Norway's Best offer that, but for some reason it is rarely taken on this forum) and the other Flam to Balestrand return with a night in Balestrand. It was the two deviations which they liked the best about the whole trip- especially Balestrand which was a big hit (again, yay, thanks for confirming that).
If you have an extra day I actually suggest Bergen to Balestrand, connection into the Glacier cruise, night in Balestrand, then next day the boat from Balestrand to Flam.
For some reason there are a few people on here who routinely pan the Bergen to Flam express boat - having not taken it, and in spite of Rick being a fan of it.
I was very interested to see the video, as I sometimes doubt my sanity reading the Forum. It vindicated my opinions completely, and I have used the express boat as well as done most parts of the route on cruises. Very refreshing to see such a vlog.
So yes, I think the express boat from Bergen to Flam is worth it, then the Flam to Myrdal and Myrdal to Oslo train. The other interesting thing about the video above was that of the traditional NiN elements the bit she liked the least was the Myrdal to Flam train. Not so much due to the scenery but due to how busy the train was.
The trick is to find one of the Flam to Myrdal trains which does NOT connect with a NiN cruise- so will be a lot quieter, more room to spread out and enjoy the ride,
But if you just want to take the train straight across that's fine too- Voss to Myrdal is a very scenic section which everyone who does the Norway in a Nutshell misses out.
It is interesting this summer that Vy Trains are adding more regional trains (as opposed to the long distance trains) from Bergen to Myrdal (some of the Bergen to Voss trains are being extended to Myrdal).