No intelligent story would try and disclude known laws of physics. Off topic but, theoretically, if we had some sort of spiritual energy, hereditary defects could easily be passed down that weren't really defects. "Oh look, if I put energy in my eyes, I can make them change color and they give me super vision!" It's not so inconceivable if you take into consideration you have a form of spiritual energy that is not proven to exist in our universe. But no one's trying to prove that so I'm rambling.

You can easily include the laws of physics because those are known laws that you cannot defy. Anime and stories may sometimes break the laws, but they still include them. "Oh look I can fly, but I gravity still exists because I can still walk if I wanted to, I can just fly as well" No one's trying to prove anything, like how Neji can have a 359ish degree field of vision. It started as speculation on how Naruto ends up on top of the frog, and the frog's summoning speed was brought up. People go, "Well gamabunta appears super fast so that's the speed of light!" It's hardly the speed of light, anyway (if it were you'd probably see the summon before the smoke appeared from the impact of it, but you don't see that so it's safe to assume it takes a little bit of time for the frog to appear)