AFAIK there are no FAA regulations or restrictions about the use of High altitude vs Low altitude charts. (Not sure about ICAO.) There are obvious differences but there are subtle differences also. The charts are designed differently for different users, High altitude for jets and airliners, Low altitude for pistons. (Whenever I fly 50 to 350 nm in an airliner I always use Low altitude charts. I don’t want to fly to 30,000 ft for a short trip. And when flying the C172 cross-country, I won’t use High altitude charts due to the performance limitations of the C172.)
Planning an IFR direct route between airport A and airport B should be easy for MSFS but the MSFS Flight Planner is not designed for direct IFR routing. IFR users have to use either the High or Low altitude routing. “None” is not an option. This does not mean that the Flight Planner is broken. A 3rd-party flight planner might work or manually editing the flight plan.
Your question about the sharp descent from 31,000 ft in the Flight Planner is valid. However, the Flight Planner is doing what you are requesting. What is your plan to descend from 31,000 ft to the ILS initial fix assuming you will be using the autopilot without using a STAR? It is possible to request a stepped descent from ATC but you are still responsible to determine when to start descent.