Generally speaking magnetic north is all that is used except when operating close to the magnetic poles.
I think perhaps you have misunderstood the application of magnetic north vs true north. Using magnetic north you can still plot the same waypoints using latitude and longitude and they have the same coordinates regardless of whether you are using true or magnetic north. The difference comes when measuring the angle (bearing) of the course between waypoints. You can measure that angle reference true north or you can measure it with reference to local magnetic north. Given that basic aircraft compass systems point to magnetic north, it makes sense to use magnetic where you can. To convert the bearing to true north is simply a matter of adding or subtracting the local variation which is the difference between mag north and true north at your location.