Yes these changes are deliberate. It was never intended that tools should infer anything from the description line. It is merely that - a description. The type 1 line and its transformation matrix must be processed by any tool seeking to replace a moved to file with its target. That way the results of a substitution should be identical to leaving the moved to file in the model and allowing the normal type 1 line processing to take place.
Chris (LDraw Parts Library Admin)