Not sure. I was yesterday flying in the Community Fly-In where the provided PLN file was set up as VFR and the sim added these TIMECLI and TIMEVER waypoints as well.
I opened it in LittleNavMap, changed type to IFR, saved it and loaded into the sim, and it worked just as expected, no aritifical waypoints.
You can try it yourself with the flight plan provided here: