Boeing think that running one pump dry for an extended period can occur if you leave both center tank pumps on if an NG has not been modified, due to the master caution logic. So we are talking about a procedure that can be used on unmodified aircraft.
As most people know there are some fundamental differences in the way the the classic and NG fuel system works. The pumps are in other places etc. Therefore there is a difference in procedures.
You are free to use whatever procedure you are comfortable with. NGs were not exactly dropping out of the air over the years before this system was introduced and to the best of my knowledge the only problems that did occur were on the ground at high ambient temperatures in South East Asia. That saga got Boeing taking a closer look at the system and recognising that there might be a potential risk.
So far that risk appears to be lower than the documented instances of gross mismanagement of the fuel system. The BA incident fuel balancing over the alps followed by aerobatics and the Qantas 'lets see what happens when the main tanks run dry' are but two examples (both classics). I would also be interested to hear the highest imbalance anyone has heard off, obviously happened to someone else!