@Merijn-1 Hi, I'm not a TomTom expert, because I'm using Garmin. But may I can help with some information.
At first: results in route planning with MRA depends on maps, you are using. As Gold-Member, you can additionally select Heere (Garmin) or TomTom map. If you set only a couple of Way Points, result of route will may differ in that maps. If you set more WP, routes may come closer to same result.
To learn, how to mitigate different route results, as Gold-Memeber you can use MRA function to compare between Garmin and TomTom routes.
Second: If you use in your Navi device (TomTom or Garmin) the option to create fancy (curvy) routes, the result is based on algorithm of device. If you export this route to any other device (or MRA), you will never get same route result. Imported route will always differ more or less, based on own algorithm of that device (or MRA).
I believe, root cause could be, such fancy function in Navi device will not create really true WP, but only so called "shaping points".
Third: If you import a route into MRA, you will be asked if to use route or track. If you select route, than all information of that route will be importet. But if (gpx, int) data did not contain enough Way Points, MRA is more or less able to calculate this route to same result as your Navi device. Mostly, you will have need of maintaining the import, by setting additionally WP.
If you select import option "track", you will get in most cases same result as in your Navi device. But after import, track is only graphical drawn line as overlay over used map. With this line, navigation algorithm will not be able to calculate; can't give you instructions during ride.
But MRA offers you a funtion, to convert this track to a route. Whit this, you are at the point as described above: you may need to maintain the route by setting additional WP.
With this information, I believe it's not difficult to learn. These days may give you enough time If you are currently allowed to travel to your work place, use your Navi and MRA and play arround...