10 Day Bavaria Trip, Suggestions for Home Base(s)?

I lived in Bavaria for four years and am very familiar with all the places you mentioned in your post. Germany has a great rail system that can get you from city to city, but then you need to move around once in a city. Munich, Augsburg, Nuremberg all have public transportation, but learning to use it will take up much time. Still, you can use it to some degree, like getting from the Munich Airport to the HBH (train station) downtown. Of course, you can walk around with a tourist map or guidebook.

I don't recommend trying to do the Berchtesgaden/Salzburg area or the Garmish/Fussen area on day trips from Munich. To do Salzburg and Berchtesgaden you need at least 3 days and about the same for Garmish/Fussen/Zugspitze.

Nuremberg is about a almost a two hour train ride from Munich, but you need more than a single day to see that city. Don't miss the
old parade grounds, site of Nuremberg trials and museums.

You can do the Zugspitze by taking the cable car or cog train from Garmish to the near top of the mountain. If you like to hike, in Summer there is a great two day hike.

In Munich you can take pubic transport to see Dachau. You can do downtown Munich on your own walking using a guidebook or map. For Salzburg, Mozart's house and the Cathedral (featured in the Sound of Music movie) and castle on the hill can be down on your own. Getting to Berchtesgaden you might look for a day tour. Not sure if the Eagles Nest is open in late September, it probably is. Late September is when the huge Oktoberfest is going on, so you will need to book lodgings early. Consider going to the fest for a day, go early when the tents are the least crowded. There is more to Munich than I have mentioned, like the old Olympic grounds and castles.

Rothenburg ob der Tauber is on the Romantic Road that runs from Wurzberg to Fussen. Several medieval walled towns are on the road as well as ancient cities like Augsburg (worth half a day for sure). You would likely need to rent a car for a couple of days.

https://www.romanticroadgermany.com

It's not too hard to see the reason for the popularity - despite the modern roots of the idea, the tour combines the historic cities of Würzburg and Augsburg with the three medieval walled towns of Rothenburg ob der Tauber, Dinkelsbühl and Nördlingen, and then finishes off with the tourist highlights of Neuschwanstein Castle and the Alps.

We will be doing this area next June and will have a rental car
Would like to spend a couple nights in small off the beaten track
In the Berchestgaden area or near Mittenwald
Any suggestions

Would like to spend a couple nights in small off the beaten track

Berchtesgaden and Mittenwald ARE the beaten track. Nice places... Mittenwald exceptional... but everyone and everyone else knows about them and will be there with you. Expect competition for rooms.

Primary interests are WWII, villages, scenery, cities.

Check out a site named thirdreichruins.com. It has photos taken shortly after WWII of many of the places that you want to visit. It then has photos of the same places taken more recently. The contrast between some of the photos is quite interesting.

Will most likely fly both into and out of Munich, so that will definitely be one of the home bases.

If you're planning to do day trips from Munich, make sure your hotel is near the central train station (Munchen HBF). Otherwise, you'll end up adding another 60-90 minutes each trip just to reach the train station that connects you to those destinations.

Nuremburg might be a good base. Has good connection back to Munich and good connections to Bamberg, Wurzburg, and RodT.

We did a similar trip a few years ago. We flew into Munich and stayed there for several days, then took the train to Salzburg for a few days, then to Rothenberg for a few days, and then back to Munich for one night before flying home. We went to Dachau and the Eagle's Nest, as well as Neuschwanstein. We did Neuschwanstein with Mike's Bike Tours which included a nice bike ride. I thought my husband and adult son would think it was cheesy, but all 4 of us had a great time on it, FWIW.

Folks have different travel paces. This list and its spread out nature would be a little too fast paced for me in 10 days.

Bases & day trips are good in that you do not have to change hotels so often. Still you surrender parts of your mornings and evenings traveling to & fro. Mornings and evenings/nights are my favorite times for sight-seeing.

Rather than adding to the list, I think I would be focusing on seeing few places but tending to spend the night in places that I really want to experience. Rothenburg and Zugspitze (for example) are different at the ends of the day than they are at noon.

I spent 5 days in Lichtenfels, a small town north of Bamberg. Very convenient train service to the Franconia region of Bavaria. We stayed in annapartment anove a wine shop. Nice central square. Lictenfels is the ‘basket capitol’ of Germany. Intetesting woven items around town. A couple of very nice restaurants in town. I had my best wiener schnitzel in Germany at some one.

I agree with Gary. For a ten day trip, changes hotels every day or every other day will be a chore. Don't forget you have to repack everything and check out and back in. IMO, a waste of time.

With a first time visit, Munich alone can take two or more days, especially if you like Museums and WW2. Nuremberg can be done in a day depending on what you can see and what trains you take. You can do most by public transportation. Cars may be a bit dicey in Munich and Nuremberg as far as parking fees.

I would cut at least one city from my itinerary, because part of the charm of Bavaria is just walking the streets looking at the architecture or sitting in a beer garden/beerhall eating a meal.