Path of War - Community Package....

[Krothos]

By RAW, you can select an archtype until a level where the archtype makes a change to the character class. This is at level 1 for most archtypes but there are some that do this at level 3, so you wouldn't need to select that archtype until that level.

My experience with archtypes is that HL will provide that warning that you saw, and then still apply the appropriate changes to the character.

You may want to create a test character with a standard Paizo class and archtype to see if you experience the same behavior. If you do, then it's probably an issue with HL and you should submit a bug report to LW. Otherwise, it would be an issue with the PoW pack which SC would have to look into.