You are going to have a bad time with such time compression rates. If I understand correctly you want this for the sub-simulator. Take a look into how it was done in Silent Hunter. As far as I can tell, they run simulation on the physics side with the same rate in 3D view, even when time is compressed. This means that you have to manually control update of your physics and your render game time. Only on map they allowed a higher time compression as at this point no physics is simulated at all - everything just behaves as kinematic bodies.
The good news is that physics sub-stepping is already doing something similar to what you need, but you have to get a better control on how many sub-steps you are going to have when you compress your game time.