
Lyee |

As they're alternate classes, don't we already have as many as two favored class options for each of them?
From Reading-as-written, it seems they are not alternate classes, but have an 'alternate class list' they cannot multiclass with, and are not alternate classes in any other way.
This is backed up that the Swashbuckler explicitly calls out that they qualify for their alternate class (fighter) feats, instead of it being implied by alternate-class-ness.

Regeaj |

One way to do favored class bonus, at least for now, would be to have the player choose one of the two classes on the Alternate Class list for their class and allow them to take the bonus for the class they chose. The choice for which class they could get the bonus from would be made at level 1 and could not be changed.

Regeaj |
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One thing not mentioned: What if a Half-Elf has BOTH classes as favored classes?
They are only gaining levels in one class, let's say Slayer. They start off as Slayer, and choose that they can get the Rogue Favored Class Bonus. Choosing Ranger and Rogue as a Half-Elf wouldn't help because they are gaining levels in neither of those classes, rather, they are gaining levels in Slayer.