As I understand it, any object that has lat / lon (a, b) under the Mercator projection will have a different meaning than (a, b) under the user projection. For example, if your user projection was polar, the object would have a distance from a fixed point and an angle from a fixed direction and would not be / lat at all. So, a way to tell your KMLLayer about a user projection would be to convert the coordinates of each object and rewrite KML.
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