This maintenance practice does seem a little strange, probably thought up by someone wearing a suit in a nice warm office who actually didn't think about the labour involved by introducing this check.
The frequency of this check also puzzles
me. The frequency suggests that there must be a lot of reported problems with water ingress and or corrosion in the fuel system
although in my career I have yet to encounter such problems.
As for using water in the fuel tanks during maintenance I must admit on our yearly inspections of the fuel tanks in our aircraft(helicopters), once all the sump pads have been removed we use warm water mixed with Lux flakes to wash out the tanks. I don't know about you but even with breathing gear on I don't fancy spending a shift in a tank with all those fumes. It doesn't take all that long with proper ventilation and a few rags for the tanks to be completely dry.(The tanks are washed rather than flooded before you all fall off your chairs in aghast!!).
Just for info our aircraft do around 100hrs every 2.5 to 3 weeks and they seem to spend more time in the hangar on check than they do on the line earning us money.