Your explanation to yourself is spot on!
But one last point, you don't actually need to "Clear route" first.
If you use "Change route" and then "Change destination", that's just the same as starting a new route from scratch, so I think it saves a button press or two.
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As for getting it to travel via a main road such as the M1, then I think that's one of the basic limitations of most sat navs, and certainly all TomToms.
Their little brains are locked into thinking about "points", so to navigate to an address, it asks you for a point on a road (i.e. the house number). If you don't give it one, it just goes to the middle of it..
So for very long roads like the M1, it has no idea of what part of it you were wanting to use. It's where "common sense" is actually very hard for a tiny computer brain to emulate.
In that situation, the workround that I use most is to let it calculate the route, then do Change route --> Travel via --> and then use "Point on map" (on the second screen of choices) to pick somewhere on the M1 to go via.
Do make sure you zoom right in though, to make sure you've tapped the right side of the motorway, otherwise it will take you round in a big loop to go past the EXACT spot you marked on the other carriageway!
Alternatively, I have added a set of "Motorway entrance" and "Motorway Exit" Points of Interest files from PocketGPSWorld to all my TomToms. These are REALLY handy, as they allow you to specify an actual junction number of a motorway to go to, or travel via.
If you can't find them on the PGPSW site, just ask, as I'm active there too.