Is this specific to Hopper, or is it a limitation of buying through Online Travel Agencies in general?
can’t speak to AA, but UA does not allow residual to be used with TA tickets. In fact, all UA non-refundable ticket rules have a restriction that if new ticket is lower, residual is forfeited. Initially, when change fees were eliminated in 2020, that rule was enforced through even tickets issued by UA itself, however, a few months later, they put in place a policy to issue residual FFCs for tickets booked through UA only. TA tickets don’t get residuals.