Adding country side with City Tour.

Yes, certainly you can do this. If you do not get some good ideas from this thread, post a separate question in the appropriate country forums to get the attention of the experts. If you review the Germany forum, I think you'll find several posts discussing pretty areas outside Munich. You may need to go back a couple of months. I know the Tegernsee has been recommended, just as one example.

Switzerland is just one incredible view after another, so it just depends on what time of year you plan to travel and whether you want to get high up in the mountains for walking/hiking or are planning just a very quick visit. Be aware that Switzerland is very, very expensive.

A great countryside tour in Southern Germany would be the Romantic Road. Here is a short tour that does some of the road.
https://www.viator.com/tours/Munich/Romantic-Road-Rothenburg-and-Harburg-Day-Tour-from-Munich/d487-285010

Also, from Munich, tours of Salzburg, Austria and Berchdesgaden, Germany are good as well as Garmisch, Oberamergau and the castles nearby.

For Paris, I suggest a couple of days in the Loire Valley or an extended tour to Normandy.

That Viator tour says it takes 10½ hrs and spends only "about 3 hours" in Rothenburg! And they don't spend the rest of the time in Harburg. According to ViaMichelin, the "Discovery" route from Munich to Rothenburg through Harburg takes 4h25 driving time, and only about an hour is on the actual Romantic Road, although most of the small roads (not motorways) in the area are pretty similar. (BTW, it's not the Romantic Road itself that is so special, it's the towns it goes through). The fastest route back from Rothenburg to Munich goes through Nürnberg and takes slightly over 2½ hrs, leaving half an hour for Harburg. I don't think 3 hours is enough for Rothenburg and half an hour is definitely not enough time for Harburg.

Much as I liked Harburg, I would skip it. Go by train to Rothenburg and give it more time. Stay overnight and the next day go by train from Rothenburg to Prague via Nürnburg and Fürth im Wald. Use a Bayern-Ticket to Furth and a Czech Rail ticket (purchased from www.cd.cz for about $13 per person) to Prague.

In 2012, I went from Munich to Prague with a Bayern-Ticket for an overnight (3 nights actually) in Zwiesel, in the Bavarian Forest Nat. Park. Zwiesel is a nice example of small town Germany, about 10k population, in a pretty setting but not a lot going on. I think you can visit the glass factories in town. If you go there from Munich, you can stop for a few hours on the way in Regensburg. If you spend the night in Zwiesel, you get a pass for the train which, the next day, you can use to go Bayerisch Eisenstein, from where you can take local Czech trains for about $9 to Prague (buy your ticket from Czech Rail in the Czech side of the station building. On the way to Bayerisch Eisenstein, the train stops in Ludwigsthal, where you can visit the nature preserve.