I've seen the same problem with UVair flight logs. Really annoying; however, you don't have to put the ETP waypoints into the FMC. If you restrict the FMC waypoints to the ATS flight plan / clearance, you shouldn't have any trouble with CPDLC/ADS.
Similar problems can occur if you are cleared 'direct to' a wpt and use the 'abeam' function for fuel checks, etc. CPDLC will send loads of unnecessary position reports. Better to copy into RTE 2 (if you have one) and use this for the abeam checks.
The best flight logs give you the basic waypoint sequence and then publish ETP/PNR info on a separate page.
Don't think I can answer your actual question though, as I've never seen a reference. As you say, it just seems like common sense.