Based on the description given in the manga (specifically "I rubbed it on the meat before boiling" [emphasis mine]) I would guess that this is not actually an effect of tenderization at all. Instead, the effect is possibly closer to that of velvetingvelveting.
The velveting technique is typically done with a thin coating of corn starch, and my working theory is that this seals in the natural juices of the meat while preventing the outer layers from drying out. Being thick and viscous, honey might have much the same effect. As a result, the final product seems more tender, but that's just because it's been more delicately cooked - not due to any special tenderizing power of the honey itself.