In a perfect world, we wouldn't be getting on a plane but if we have to, we will.
No Need. Germany's rail system is extensive and highly developed. You can reach Caen, FR by train but may want to get a car there for visiting the Normandy beach towns.
Also, any opinions on what to prioritize when we visit Germany would be great.
You made your priorities clear. History surrounds you wherever you are... Much of Germany was once part of the Roman Empire. It happens that Germany's oldest city, Trier, was an important Roman outpost with plenty of history you can get eyes on even today. And Trier is near the French border, less than 4 hours from Paris by train. Rick Steves covers Trier. More info on Trier:
https://www.trier-info.de/en/places-of-interest
The Mosel River runs through Trier and the whole river is dotted with old-world wine towns and castles from Trier to Koblenz. This is one of Germany's most scenic train routes. Sounds like somewhere you would like. Most towns have train stations; those that don't have bus connections to nearby stations. Biking along the river from town to town is and easy and popular way to take in the scenery.
Mosel River scene:
https://www.zughalt.de/wp-content/uploads/2011/10/DB11321.jpg
Cochem:
https://img.fotocommunity.com/reichsburg-cochem-mosel-d3c1f03b-fafb-44ea-ae46-aa69ba7ebdb7.jpg?height=1080
Beilstein:
https://img.fotocommunity.com/beilstein-an-der-mosel-271c065b-2100-4db9-98ef-90339e58e39d.jpg?height=1080
Mosel towns and villages:
https://www.mosel-inside.de/en/travel-guide/mosel-villages.html
Are traditional BNBs a thing there?
Fewer and fewer in number as the years pass. You can still find some homey places that come with breakfast, often in hiking/biking areas where outdoorsy types need simple accommodations - areas like the Mosel Valley and the Rhine Valley (which meet in Koblenz. See map.) They are called "Privatzimmer" or "Private Gästezimmer" or sometimes just the broader "Gästezimmer".
https://www.orslev-cykelrejser.dk/upload/images/cr/tyskland/mosel/model%20og%20rhinen%20-%201%20ny.png
Here's a Privatzimmer in a Rhine Valley town called Osterspai, near the Rheinsteig hiking trail:
http://www.metz-braubach.de/html/bilder.html
There are also Guest Houses ("Gästehäuser") operated privately or by businesses, like this one in a local bakery in the Mosel town of Bullay:
https://www.cafe-baeckerei-goergen.de/
Castles/castle tours:
Mosel Region: Burg Eltz
Rhine Valley: Marksburg