Doomsday Engine

I think the whole offset part is broken.
It offset's the model from the camera and not the 0,0,0 map coords

-------
Model {

ID = "ghostboneframe1" Scale XYZ { 1 1 1 } Offset XYZ { 0 400 0 };  # The offset is the actual map coords.

Skin tics = 5;

Md2{ Flags =  "mif_sphere" File = "ghostbonepath2.dmd" Frame = "0" Skin range= "5" ;}
-------
according to the wiki the model should be placed at the coords X=0 Y=0 Z=400
But it is not, it is placed 0 x units 0 y units and 100 z units away from the camera 
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Model {
  ID = "ghostboneframe1" Scale XYZ { 1 1 1 } Offset XYZ { 4282 100 3511 };  # The offset is the actual map coords.
  Skin tics = 5;
  Md2{ Flags =  "mif_sphere" File = "ghostbonepath2.dmd" Frame = "0" Skin range= "5" ;}
-------
And this should be placed at X=4282 Y=3511 Z=100 in the map coords
But it is not, it is placed 4282 x units 3511 y units and 100 z units away from the camera

ok, nevermind, forget about the last followup/comment I added. fixed positioning was my fault.

The offset order is still broken though

Not a bug. The sky model renderer allows for models to be offset relatively from the camera so that it is possible to create faux perspective, so that objects move around the viewer at different rates depending on how close they are to the camera.

It sounds like you are wanting to use a sky model to "extend" the map geometry itself by positioning it precisely within the map. The sky model renderer hasn't been designed for that but if you set the Map Info->Sky Model->Offset Factor to {0, 0, 0} and then use the Model->Offset to position it, you may have some success, otherwise additional functionality will be required.