Also worth noting that currently, any change that you made in the flight plan “after” you start your flight from the world map will reset the cruising altitude and assumed you’re on the Low-Airways. Which is why the ATC keeps telling you to fly at 16,000 feet or so.
The only way for the ATC to assign you the right cruising altitude as in the flight plan is by making sure you have a complete flight plan from departure gate to the arrival gate. Re-selecting the depature gate and the arriving gate from the drop-down will also assign you the active runways into the flight plan with the most appropriate approach.
Then when you switch to IFR High-Airways in the world map. Make sure you also assign the Departure Pattern (SID) and the Arrival pattern (STAR) from the world map as well. This is so that you have a full pattern into your flight plan, and the ATC will take this into account when assigning you the departure runway. As well as the approach at the destination.
That way, once you have all the flight plan completed in the world map, when you start the flight you don’t have to make any changes to the flight plan. So that the Copilot assist doesn’t think there’s a change in the flight plan, so it doesn’t request a new flight plan clearance which sets you to an IFR Low-Airways cruising altitude.