I have to respectfully disagree with that stuff! Firstly, the Mary Rose wasn't already in battle. It was going towards the battle, still in sight of the shore when it turned heavily and, weighed down by the extra men added to the roster last minute along with open gun ports in preparation, leaned too much and flooded, resulting in the sinking.
The cases of bows were found at various locations within the ship. The way the wreck was discovered meant that half the ship was found just as it was when it sank. Everything was found where it would have been, so point 5 doesn't quite work I'm afraid!
Points 1 and 3 are kinda in the same vein, and neither work out, as nothing was really lost. Items right down to shoes, leather thongs, buttons, jewelry etcetc were all recovered so if hundreds of bows that weren't in the crates had been onboard, they would have been found too. Some of the bows were actually found loose and not in crates, so perhaps they were being carried by archers towards the upper deck?
I think most of your points are based on the fact that the ship was already engaged in battle, which according to most accounts it wasn't. In fact Henry VIII was watching from the castle when the ship simply turned to tack into the wind and just sank. Hope that clears it up a bit?