My own thoughts are that something like closing the throttles to flight idle at some reasonably high altitude in the landing regime would increase the LP pump discharge pressure. In turn, this would decrease pressure at the impeller area of a centrifugal pump, as this pump is. I know this is very counter-intuitive (so pump engineers tend to be specialists). Under the right adverse conditions, a decrease in pressure within the fluid fuel column could cause ice crystals to precipitate out of solution or entrainment, where before the water content may have been causing no problem.
At low altitude, even if the pumps would have encountered such conditions as you describe, suction feed bypass valves in the engine feed system would have opened to feed the engines. Those are check valves and not sensitive to the conditions the pump impellers are subjected to according to your explanation. No ice crystals would precipitate out of solution at those suction feed bypass valves with the fuel quality being within specs as tested by the AAIB. A scenario whereby both the boost pumps and the suction feed bypass valves would have been blocked by ice therefore seems very remote. This could perhaps have occurred with a much higher water content in the fuel (way outside the required specifications) than was actually sampled from the fuel in G-YMMM's tanks.
Just my thoughts, something other than ice in the fuel must have (partially) restricted fuel to the engines to less than required. It may have been a "manifold" of circumstances (holes in the swiss cheese) interacting in the same slice of time that made it so. Something not recorded.
Regards,
Green-dot