Let me give you a little perspective.
I owned a bicycle shop for over 30 years. (several years the largest shop in the state) and personally I have worked on thousands of bicycles. Most of my mechanic work was done in the days of caliper brakes.
I have a Dahon Mu D10---modified a little--- in my front entryway that I put 40 miles on yesterday. Yes it has v-brakes but it also has the mount for fenders/caliper brakes.
The mount for caliper brakes has always been a simple tube between the seat stays of a bike. look at any road bike as to what the brake is mounted on.--
I guarantee you that any caliper brake you mount to the brake/fender mount on your Dahon Mu frame will not damage the frame if you properly install the caliper brake---unless you crush it by tightening the bolt beyond reason.
You are correct the caliper brake if not mounted with a recessed bolt will have tubing matching washers to match the curve of the tube you are bolting to.
Good luck with your project.