It's not really a problem if the designer and operator accept the additional manpower, maintenance, and equipment requirements. "We've always done it this way" does not necessarily make it the smart way to do it.
I've been a barge engineer responsible for stability of the barge along with all it's systems to keep the drilling rig running. Those systems included fuel & water to keep everything going. My boss was former Navy and we adopted systems that he knew including centrifuges. We used centrifuges because we had fuel quality issues that we couldn't control. Receiving diesel from workboats puts one at a slight disadvantage to say the least.
On another note, consider that ships have historically been allowed to discharge oily water when on the high seas so a little pollution is no big deal for the fuel over water gang.
As for your comment on breaking the back of a barge, all vessels must be loaded correctly. Some vessels are easier to manage than others but weight and balance has to be considered similar to aircraft. I've been to school and performed the calcs for offshore rigs. I'd rather deal with weight distribution problems rather than repairs due to water in the fuel to my diesels...
Now consider that Henning is a license Master with broad high seas experience. Keep his comment in context while respecting his knowledge and perhaps you'll understand that he sees little need for additional manpower and maintenance to deal with a fuel-over-water system. On the other hand, the Navy has historically desired large crews although that is now changing.