They’re trying to capture the consumer surplus. Normally, a seller can have either high margins and low volume, or low margins and high volume. The retailers wet dream is to get the benefits of both. If the reward program profiles you as someone who buys coffee at $4.00, but not at $6.00, you’ll get coupons for coffee that the people who buy coffee every week regardless of price won’t get.
FWIW, I’ve found stores that don’t even have rewards cards frequently have lower prices than their competitors’ reward card sale prices.