We have noticed that when doing a regular query of a lrs enabled map service that the service will always return the geometry with the Z and M coordinates and you are trying to output in geoJson even if you have the flags to enable Z and M set to false. If you change the output to HTML or JSON it will not give you the Z and M like expected but switching to geoJSON will bring those coordinates back. We are using R&H version 10.7.1.