My X1 has not been started in a while. Almost all of the oil has drained into the crankcase. (about a cupfull left in the tank)
Is it safe to start it or spin it over in order to get the oil back into the tank, or is there any way to drain the crankcase?

Yes. Wet sumping when sitting for a while is normal.

Always check oil level after the bikes been warmed up, not before. Do not overfill. If you get the oil level too high in the bag, it'll just blow the excess out of the breathers.