The different, more beefy animation of Entrench is very much intentional as the ability changes the rules of the battlefield dramatically.
While entrenched, the Sniper has tremendous defensive bonuses, and cannot be interrupted or otherwise controlled and the very visible fortification effect around the normal cover created by this ability is necessary to signal to other players that they're now engaged in potentially a very one-sideded confrontation for the duration of the ability.
Abilities that dramatically change the rules of the battlefield need to be broadcasted clearly to all participants to avoid confusion (e.g. if an Inquisitor brings up his static barrier that absorbs incoming damage, you see the very visible lightning shield flare up around his character to allow players to understand why their attacks are not working).
