Most of the current aircraft certification standards prohibit a fuel pump drawing from more than one tank at a time. So far as I know this is for the reason I stated earlier - if an imbalance (say) leads to one empty tank and one that is partly full, the pump will tend to draw air from the empty tank causing the engine to stop with fuel remaining on board.
This wasn't historically the case, and since aircraft are usually allowed to continue operating subject to their original safety requirements older aircraft are able to continue flying legally with a "both" option on the tank selector valve.
I don't think now I'd be able to certify a new type anywhere in Europe (at-least) with a both selection available to the pilot.
G