When creating your flight plan, are you selecting VFR or IFR in the EFB ?
There is a similar report where custom waypoints are not loaded to the world map & avionics if VFR is selected: Tablet flight plan not representative of what is shown on the planner and avionics of certain aircraft - #4 by DementedCorn327
I did a test with the same FP provided in the other report with the PC-12/PC-24 and custom waypoints are loaded if IFR selected:
