However, rules=physics means that all rules must apply equally to everything that exists within the setting. You cannot possibly achieve that goal within the framework of an RPG. Exceptions have to be made and will be made constantly. Omissions will likewise be made, simply because the DM is assumed to fill in those gaps.
No. You simply have to stop ripping of LOTR and cheap fantasy novels when creating your plots/world but instead look at the rules beforehand and write a world which takes the existence of this abilities into account. And if you as DM overlooked something which lets the PCs overcome a challenge then let them. and bring on the next challenge instead of altering the physics of the game world just so that this doesn't work.
You effectively arguing that because there are no rules covering it, no one could possibly swim in 1e D&D. Since 1e lacked any skill based mechanics (other than thief abilities) there is no possible way that anyone could make a sword in that system.
No, I'm arguing that when the rules say that everyone can swim with a speed of 30ft then everyone in the setting can swim at that speed and that racing through water at that speed is normal for this setting. What should not happen is that in combat the PCs (and only the PCs) can swim at 30 ft each round but outside of combat they are much slower in th water.
Likewise, in 3e, since there is no penalty for not sleeping, my character in your world should never have to sleep. Makes guarding a whole lot easier I suppose.
Don't you get fatigued when you don't sleep?
What you should do now is either make a rule that everyone has to start making Con checks after X hours of being awake or that really no one sleeps in the game world. What you should not do is to arbitrarily inform players that they are tired now because they have stayed awake for too long or have some people in the world sleep and some not.
The only way you could create a system where rules=physics is if you place hard limits on what the players can do. In order for the system to work, you would have to forbid any action that isn't expressly covered by the rules. In other words, you'd have to turn the game into a video game. That's precisely what a system where rules=physics looks like. You cannot step outside the phyics in a video game ever.
As I said above, you can make a rules=physics world by simply not ripping of LotR and the medieval time periode anymore and let the PCs do whatever they want even if it ruins your adventure.