When the opponent changes something in the past, wouldn't you have been there to respond to it? Why do you need to use chronoenergy?
Also, why is it that characters can avoid a Tele-Frag teleporting somewhere they've never been, but don't so much as check to see if anyone was standing there when they time travel?
One, you're an Achron, that means you can see the future, change the past, etc, but you have to move to that time. Two, there is no telefragging in the game and units can't see back in time to check they aren't about to chronoport on top of someone, it is the job of the player (who is an achron) to do this.
As the previous troper mentioned, the player is an achron. This means that you wouldn't have been there to respond to it as you are basically outside time itself. However, I do find the chronofragging to be a bit of fridge logic myself. Telefragging was rebalanced out of the engine to prevent games deteriorating into fragfests, but chronofragging still persists because of handwavium.
From a balance perspective, it prevents chronocloning. Send the same unit back in time 10 times; it'll take a lot more planning if you have to do it while accounting for chronofragging. Chronocloning wrecks the game balance, because it means a single unit with a chronoporter can potentially defeat an army.
The fluff reason is simple enough. When a unit is using the teleporter, they can check and see if there's something on the other side and adjust accordingly. When they chronoport, they're relying on the achron to figure their position and time. They can't perceive time achronaly, so they are entrusting themselves to the careful orders of the achron. Only you, the player, have the point of view to prevent chronofragging; when you screw up, people end up at the same time, the same place. (Unless, as expected of a good player, you drop back 10 seconds and go "Hold it, nix the porting.")
How come the Human importer can hold reserves (unequipped humans) and teleport them all the way across the map to a factory/armoury/macrofab via its internal teleporter (this is how they work from a story perspective) but the Vecgir (who are masters of teleportation) have to have an Annex directly adjacent to the Depot? (When you build a vehicle in the Depot the infantry that pilots it is built first in the Annex then teleported into the Depot to get in the vehicle the Depot builds for it, this way when the vehicle is destroyed the infantry ejects and keeps fighting). Can't the Annex teleport the infantry it makes across to the Depot wherever it is?