Hello, I hope I didn't just overlook this, but I can not find exactly how archetypes interact with the new alternate class features in the Operations Manual.
An example, the Envoy's alt class features sometimes trade out the Skill Expertise ability and their 9th level trade out for archetypes is the second skill from that ability. How does that stack? Does it even stack at all?
Sorry if this was answered elsewhere.
My own interpretation is, you can swap out an alternate class ability to take an archetype just fine. If the archetype replaces Ability X, and you've swapped Ability X for Ability Y, you just lose Ability Y for the archetype instead ( though why you'd intentionally take an ability you'd just swap anyway is unclear ).
The only problem is if a modified class ability replaces the standard class abilities, in a way that would have the archetype swapping part of an ability. If you have Ability X in place of Abilities Y and Z, and the archetype wants to replace only Y? Well, I suppose you could voluntarily accept losing even more than normal, but that's kind of unlikely.
Lesson learned? Don't apply an alternate ability for something you are already planning on replacing with an archetype.