Hi Patchouli -
Some more comments on your itinerary. I still think it is a good one. This attached map/ boat schedule shows how you could stay at many places along the lake shore, some of which are quainter than Kreuzlingen. Kreuzlingen has good rail service, though.
The lake boat service to Friedrichshafen for the Zeppelin Museum should be considered for your "jet-lag day." You may need a visa for Germany?
Kreuzlingen is on Lake Constance, at the mouth of the Untersee, which can be considered a wide spot in the Rhine river, or, a part of Lake constance. By the time you get to Stein-am-Rhein, it is definitely the Rhine river.
Everything west of there is on a branch of lake Constance called the Untersee, or along the Rhine river.
I was confused by your description and naming of the routing until I followed the link you provided.
It appears that the tour company whose itinerary you use as a model has chosen the name "Aare Route" for their own choice of routes. Switzerland also has an official "Aare Route", which is only part of your route.
Switzerland has National Bike routes. Switzerland Mobility offers exceptional detail on those routes, including maps, height profiles, "where to stay" etc.
The route you have descried includes part of route #8 ( The Aare Route) and Route #2(The Rhein Route.)
The Swiss national route #2 may pass through some stretches of Germany going from Kreuzlingen to Schaffhausen. The border wanders back and forth along the river. Don't know what the route of the tour company does.
If you follow those links, select altitude profile, and scroll down to the proper section of the route, you can see how hard you will have to work along the way. ;-)
See attached images for clarification on the geography.
A couple show typical landscapes along the "Unter."
I also threw in a couple from Aarberg, whch happened to be handy on my computer .
Some others will follow, later this week.