unfortunately, this kind of block protection system has too many flaws and is too costly (in performance) to ever implement nicely. If it's a seperate mod that has to do this, then it has to scan and keep data on every single block you ever place or break.. if it's every mod doing this, then you've shot yourself in the foot as not every mod wants to put needless features in their mod that would only slow down the performance.
I don't believe this would cause any performance issues. Last I heard, Thermal Expansion strongboxes are no more or less performance intensive than a vanilla chest. Nor are the forestry apiaries/bee houses performance killers. All I'm envisioning is having both the strongboxes and the apiaries use a common library so that thermal expansion itemducts can insert into and pull out of apiaries set to private mode and some hypothetical future item transportation mod can connect to both.
If a mod author doesn't want to deal with it, he won't have to. All that would happen is that his classes wouldn't extend or implement classes from the protection library. Which would in turn make it real easy for another mod to tell that his mod items are not implementing protection. And vice versa, which means that if a mod author creates an item that can be used to grief, it's much easier to figure out what items from other mods it shouldn't affect. Much of the same thing currently happens, which is why the portal gun doesn't work on warded blocks; but it seems to be reliant on ad-hoc communication between developers, rather than a standardized library.