It's classic overloading of the ends. A steel ship doesn't hog as much as a wooden ship does when the ends are overloaded, so it doesn't get noticed until it breaks.
The material matters not. On large vessel one performs a simple loading curve v buoyancy. Like the image on the left. And from this data we can get the shear forces, image on the right. The sequence of loading in the operating manual that the Capt must adhere to is based upon this type of analysis. The maximum loading condition dictates the structural arrangement.
The hull girder must have a modulus that can withstand such a load. This is the structural "EI". The I = the second moment of inertia and the E, the material property.
The response of the hull girder from an applied load must be within safe limits.
The flexing is a result of what the designer has used as their safety limit coupled with the material of choice. However, if the hull flexes too much WTB doors etc will pop out, WTBs become prone to cracking and leaking, main structural girders/longts can crack and of course the fatigue aspect. Thus flexing is a structural consideration whether within safe stress limits or not.
So a carte blanche statement of wooden ships flexing different may or may not be true, but also may or may not be depending upon the type of boat and the loadings and then one must compare like for like with a steel one. Since the criterion of max deflection would be the same for both vessels, regardless of the stress values.
If there is a problem with large wooden vessels, then the analysis has either not been done properly or simply not done at all.