Why are Mundra's the only thing that suffer from lag?

[Kaisha]

1. How come benediction/hallowed ground go on cooldown often when your target/yourself ended up dying?

CDs apply immediately, and the skill waits for the animation to complete, then applies the effect. It's why you see people getting healed for full HP after having died, since the animation was still playing out as the player died. They can tweak this on a per-skill basis though as evidenced by them making HG take around half a second less than it used to before the effect was applied.

Same rules go for the enemies too. It's why you can kill bombs at the tail-end of their self-destruct animation and no one receives damage, or the Mega Flare in T9 not dealing you damage until the animation finishes, even though the damage for the attack was queue'd at the start of it which you see by the LB bar shooting up immediately.

2. There is no "animation" for stepping into sacred soil. It takes a full 1-2 seconds often when you place a sacred soil for the buff to take effect.

Soil relies on the universal server tic for buff/debuffs before applying.