Is it an issue if I change my payout from BTC to BCH at anytime? I think getting paid in BCH works better for me because of low transaction/miner fees compared to BTC's high transaction/miner fees. Am I missing anything if I do this? What is the threshold payout for BCH? Is it the same as BTC (.01)?

Thresholds are the same; aside from decred; which is noted on the main page.
generate a new unique BCH address, and select payout in that; but that is assuming BCH is on the list of coins the pools actually mines.
Crackfoo can confirm.