So, there's discussion in the GM thread for The Dead Roads about the planar traits of the Boneyard and what its timelessness means if you decide to use it. I'm not concerned about that right now, but it's still on topic here.
I'm thinking about what other things PCs have that may be different. The player's guide warns about the lack of animal companions, but there are other abilities that should work differently.
For example, I'm going to have a player play a haunted bones oracle. I plan on having the haunted curse simply not function while they're in the Boneyard, since the spirits wouldn't have followed him getting blasted into the Boneyard. (He can keep the cantrips the curse gives.) Plus it'll be fun to see how he reacts. His first level revelation is effectively speak with dead (after I dropped the hint that controlling undead would be less useful at the beginning than he thought), so that's also in a weird place. I'm going to let it work since the spell says nothing about interacting with the body's soul, and I need to let the player have his abilities.
Any other weird spirit-related abilities that can be changed in interesting ways?