[RPG] Is gaining Fly as a class skill with the Feather Subdomain supposed to replace gaining Knowledge (Nature) with the Animal Domain

The word include indicates a subset: every element that is included appears in the including set.

So the statement about the cloistered cleric’s class skills is that the given list, “Decipher Script, Speak Language, and all Knowledge skills (from the Knowledge domain, see below),” is a subset of the full set cloistered cleric class skills. This explicitly does not tell us whether or not this is the complete list: the word includes means that these skills definitely are present, but does not say whether or not anything else is also present.

However, the statement that the class operates as normal for that class unless otherwise specified does tell us about the complete skill set: it also includes the original cleric skill list.

So the complete list must include both the original cleric skill list, as well as the specifically named skills. They are, in effect, added. Which is consistent with the description of how skills may be changed: variants may list “Additions or subtractions from the class skill list,” but the rules do not allow for the possibility of outright replacement. Only additions and subtractions are allowed. Since nothing in the cloistered cleric description explicitly subtracts any of the original cleric class skills, the cloistered cleric has each as a class skill.

Would it have been clearer if they’d just said “add”? Yes. I don’t know why they didn’t. But despite the lack of clarity here, the rules still amount to the same thing.

TL;DR: Cloistered clerics have all the cleric class skills, plus a few more

As an archer, you need to get your bow feats as quickly as possible. Consider being human for the extra feat. You might have chosen to be elven to get weapon proficiency (longbow), but I think you're also getting that from your worship of Erastil. (And, as far as I can tell, Erastil is not a specifically elven deity?)

You might consider swapping your Strength to 16 and your Wisdom to 14. You won't need that bonus third-level spell for a long time, and it's better to start with high strength than to try to increase it later. (If you get a belt of strength +2 later, you'll have to upgrade your bow to make use of the new strength score.) Having a higher strength also means you can carry a melee weapon, just in case.

You might consider swapping your Law domain for Plant domain. Plant domain gives you entangle at first level, which is really nice for an archer. (Your druid can also cast entangle, but your druid has a lot of choices and very few spell slots.)