The distrust of individual scholars found in science is in fact an example of aligning individual incentives, by making success and prestige dependent on genuine truth-seeking.

But it's a big leap from "there are some big examples where aligning people's self-interest with the common good worked out well" to "a good moral system should never appeal to anything other than self-interest".

The claim is not so much that moral appeals should never be used, but that they should only happen when strictly necessary, once incentives have been aligned to the greatest possible extent. Promoting efficient giving is an excellent example, but moral appeals are of course also relevant on the very small scale. Effective altruists are in fact very good at using self-interest as a lever for positive social change, whenever possible - this is the underlying rationale for the 'earning to give' idea, as well as for the attention paid to extreme poverty in undeveloped countries.