Custom configuration in sketchbook folder -- how to use default arduino core?

Have you tried moving the file from

%Sketchbook%\hardware\arduino-addons\boards.txt

to

%Sketchbook%\hardware\boards.txt

I also notice that some boards.txt files use the syntax:

atmega8noxtalfast.build.core=arduino:arduino

I'm not sure what that does but it might do what you want.