I have done exactly as you described on more than one occasion. In my experience this sometimes causes headaches for the employees at check-in or at the gate, but eventually, after initially insisting it can't be done, and sometimes after asking a supervisor for help, they always get it sorted out.

Just today, I called and was able to book my second seat in a way that the phone agent assures me will eliminate problems, as it is linked to my original reservation. I'll find out in a few weeks if she was right.