Right… I have done some testing, and TLDR I can’t get it to work reliably.
For this test I was using the Fly-In Friday plan for Guyana & Suriname which can be downloaded here: Eugene F. Correia Intl to Zorg en Hoop Airport. This is a 2020-format .pln file which has 5 custom waypoints, grouped in two groups around the departure and destination airports.
I used the FlightFX / Marwan Gharib HJET for this test. This has the 2020-latest G3000 avionics.
Long story short - I can load the .pln and send the route to ATC, but the five custom waypoints are replaced with two in the aircraft avionics. It looks like the custom waypoints are too close together and are being merged somehow.
Also: when I send to ATC, the world map airport selection changes to the start airport and the current live runway is selected for departure. I want to start cold and dark at parking, so I select a parking spot in the world map. When I do this, all of the intermediate waypoints are removed from my plan, and the EFB shows a suggested routing instead and also adds VFR departure and approach procedures. Which is fine for a proper flight planning session, but not at all what I want.
I re-load the .pln into the EFB and Send to ATC again, and then I get the full route and remain at the parking I previously selected. But when I enter the flight, I find that the 5 custom waypoints (which are all displayed on the world map) have become 2 custom waypoints.
If I swap for the default Longitude and follow the same procedure, I get all of the custom waypoints in the flight plan as expected.
I also tested with the Kodiak 100 which has the current 2020 G1000 avionics, and the results were the same as for the HJET except that the custom waypoint names for the merged waypoints were different.
I also sheep-dipped the .pln via LittleNavMap and exported to 2024 format, and tried all of the above again, and got the same results.
Basically, there’s no way to get a .pln with all custom waypoints intact into a 2020 aircraft that I can find. The EFB flight planner is focussed on flight planning - which is the whole purpose of it, of course - but IMHO there needs to be a way to just load a .pln and go, like there is in 2020 from the world map.