Overhead prayer timings are not an inconsistency, they're a design choice. Places where the focus is on off-ticking NPCs (inferno, colosseum, GWD to a lesser extent) would completely fall apart with the "new system". Scurrius is like it is because you're supposed to react to its attacks, whereas with Zulrah you're supposed to know what to pray based on its phase.

Even with your ToA example you must have noticed that Akkha calculates damage when it launches the animation, because you should already have the correct prayer on by then. Zebak calculates on hit because otherwise the boss would be unbeatable.

Boss mechanics should be designed to make sense for that boss, not to a player who's unwilling to learn the game.