The problem with the Ark isn't the proportion of the dimensions. It's the structural strength of the material the vessel is made of.
Wood is simply not strong enough by weight to withstand the flexing and twisting (hogging, sagging, etc.)that a vessel in open water is exposed to. The more stress that is applied (which is proportional to the size of the vessel) the more material is needed to withstand the stress. The ark as described in the bible might survive if it was a single solid block of wood, but trying to put enough empty internal volume to carry all the cargo would weaken the structure to the point that it would break up in seas more that a foot or two high.
But it would be very stable until that happened!