"...where would YOU go for a one week road trip week from Munich?"
First off, the pick-up location... You will return the car in Munich - but your cruise ends in Passau. If I wanted a car (which I never do in Germany these days) I would pick it up in Passau. It's unclear to me why you would prefer to travel to Munich (by train I suppose) first and then rent your car in the middle of a big city like that - unless you have already planned some time from that week in Munich and will pick it up later on after your Munich stay. Is that your reasoning? And when you return the car... it's not necessary to drive it into Munich, either. You can drop at the airport, or possibly at a town nearby like Freising (where many spend their final night and then shuttle to the airport.)
Most travel agents IME have traveled in Europe previously, but such travel rarely informs their daily duties... Has your TA done a road trip around Bavaria? Does she have personal experience in those B&B's that she can book for this area? It would be unlikely that her experience matches your plans.
They have a lot of resources the average individual does not have as
well as discounts due to their many affiliations. They can reduce the
effort and also provide me with many more choices.
If I were a TA I would book you in places that offered the healthiest commissions - that reduces your choices and likely means discounts are illusions. I think most posters on this forum (at least those with experience at German B&B's and private accommodations like apartments) will tell you that you'll find more choices and lower prices if you independently peruse the local tourist office websites for accommodations; many or perhaps most of those are accessible in English.
Garmisch-Partenkirchen is an alpine town you might consider, one that invites individuals like you to book with them in English - it serves as an example of what I'm suggesting; here's the local TI's search page:
https://booking.gapa.de/garmischpartenkirchen/en/accommodation/search
Try narrowing the search to private rooms, pensions, guest houses.
If you find something attractive, you can google the address or establishment to check reviews, if you wish. (I've often booked blindly in Germany over the last 40 years - standards are high as a rule - and I only once booked a dog.)
Contacting owners directly by email means you don't have to concern yourself with time zones and phones.
Anyway, it seems to me you can ask for recommendations from your travel agent in this town or that town, then check her results against what you are able to find on your own at sites like the Garmisch-Partenkirchen site (or booking.com or other common engines, which also offer B&B's.) Maybe you accept some of hers, maybe stick with the ones you find...
It's always a bit of work to do your own searching, but it's more likely to turn up places that meet your personal expectations.
You may be interested in previous discussions on the question you raise:
https://community.ricksteves.com/travel-forum/general-europe/using-a-travel-agent
https://community.ricksteves.com/travel-forum/italy/travel-agent-yes-or-no
https://community.ricksteves.com/travel-forum/general-europe/to-use-a-travel-agent-or-to-not-use-a-travel-agent-that-is-the-question
There are so many places you might visit in a week that you really need to be specific about what kind of experience you want, if possible.