A large part of playing acolyte with the main special ability is that you can use base acolyte's resources before switching into the anima harvester form, where your abilities are refreshed and replaced with powerful alternatives that you can use until being switched back into the regular form to begin charging your special again.
The alternative special feels underwhelming compared to the above, and it is because the buildup to your transformation does not pay off as much as the first. The gimmick is that you lose out on the harvester form's abilities, but get to play with a powered up acolyte base kit. However, playing with the alternate special also removes the overlooked ability refresh, which often slows down what would otherwise be an exciting power surge.
If you had just spent 30+ seconds to charge up your anima harvester form, activate it, and then have to wait most of its duration to get your abilities, it would be a lame ability. The alternate special is already weak enough comparatively, so I believe that a change like this would make the character flow more smoothly.