I believe this is to do with the momentum of the aircraft after the impact with the water.
Imagine a fixed-gear tricycle such as most basic trainers. If you were to flare as you impacted the water, the first part of the aircraft to impact would be the main wheels. The aircraft's momentum would then force the nose of the aircraft down fairly violently - a bit like landing with the parking brake on. This could cause substantial damage to the aircraft, which would mean it's less likely to float and/or stay water-tight.
The effect would be less pronounced with retractible undercarriage - but even with the gear up, if you flare, the back of the aircraft will be landing first, and the momentum will force the nose down violently into the water.
If you "fly the aircraft in", the nose will impact first. The momentum of the aircraft will try to cause the tail to continue moving forwards - and therefore up - while gravity will cause the tail to go down. These two will cancel each other out to a certain extent, and the overall effect will be a much smooter arrival.
Like you, I've never tested these theories, and I have no particular desire to! It would be interesting to hear from anyone with practical experience...
FFF
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