If you fail to design your mod in such a way that people can't abuse it, thats mostly your fault. Why should people intrinsically know how you intended a boss to be done, and not kill it in the intuitive and easy way the game provides?
You say the bosses are challenging when strategies exist that make them complete pushovers. Thats your fault, not mine for using these strategies.
No, its YOUR problem to make it so that it cannot be done.
People (me included) use mostly the way of least resistance to get through stuff. There is no morality involved there
It is not, thats my point. You can always intentionally handycap yourself. I could for instance kill the ender dragon with nothing but my fist after the crystals are down. While thats possible, and quite challenging, its also completly useless, just like using anything then the most effective strategy you can come up with to defeat a boss.
Nothing to do with that
No. If you make a mod, you make it with minecraft code in mind. If your mod ends up not working properly, thats caused by the fact that you didn't program with minecraft code in mind properly.