All interactions through the remote control interface don't take the surface of helipads or helicopters into consideration. The map marker feature isn't affected though.
This affects scenarios where there are helicopters or helipads on different surfaces; if I open the helicopter remote UI in such cases I will still get a view for helicopters and pads that aren't on the current surface, but their camera view will show the location at the corresponding coordinates but for the wrong surface.
This results in wrong interactions, for instance if I'm on the current surface closer to the coordinates of an helicopter that's on a different surface, the operation of calling the nearest available helicopter will summon an helicopter of that other surface and send it to your coordinates but applied to that other surface.
The same can happen by manually asking a helicopter on a surface to go to a helipad on a different surface, since the UI makes such interactions possible.
This is particularly problematic in popular mods that use multiple surfaces such as Space Exploration.