Hi bro,
By the way its Chaeto, short for Chaetomorpha.
Biopellet biologically removes Nitrates through bacteria while by Cheato depends on the algae to absorb nitrate for its growth; there isn't a single method that is best, it all depends on your budget and system.
In my personal opinions, most reefers fail to realized that in order for Cheato to removes significant nitrates it needs to be growing / thriving. In order to them to be thriving, you need to have sufficient lights to encourage photosynthesis therefore promote growth.
It depends, if your biopellets is so effective that it removes all nutrients (Ammonia to nitrates to phosphates) them macro algae will die but the chances are slim. This is because macroalgae are not single nutrient obligate feeders.
Most reefers are worried about algae going asexual, that is they turn white and die-off thereby releasing the absorbed nutrients back into the water. But this situation usually happens to Caulerpa (Nuisance) rather than Chaeto. Further to that, this situation can be remedied by lighting your macroalgae 24/7 or frequent periodic trimming.
From your post, I gather you have decided on biopellets, thus I will not dwell on macroalgae to confused you further.
Do share if your experiences after installing the biopellets.