Ernest switched the upvote from being boosts to favourites shortly before the Reddit exodus, he did this to better align with Lemmy.
Boosts and Favourites are both wider fediverse things - using them keeps compatibility there.
The switch is implemented in hot and top sorting (as you note I think a upvote/favourite counts 50% of a boost), but it sounds like reputation wasn't fixed at the same time, for now reputation is boosts less downvotes which Ernest himself has acknowledged doesn't make much sense.