+1, would then allow Remote Player Waypoints for Xaero's Map to show players on the Y-Axis aswell.

This is implemented for player markers. I'm not sure how much merit there is to add it for others, as it's not relevant for squaremap itself. I don't see addon authors doing much beyond setting y=0 for most cases given it would only be used by external mods reading the squaremap data (not to mention adding this in a non-API-breaking fashion would probably be ugly).