In the Box example, an admin can globally alias rm="rm -i" which means that rm -rf * will still prompt for deletions. If you really want to blindly kill everyting you have to /bin/rm -rf * Similarly GUI based programs can have command line arguements that cause them to run completely silently.
In general, you build your program to suit your clients needs and put in exceptions if you have clients with varying needs. Make it easiest for the majority. This isn't that complicated once analysis has determined who the clients are and what their needs are.