Fix Time inconsistency after substepping loop

[Jondolf]

Objective

There are currently two issues that cause Time to be inconsistent, even with a fixed timestep:

1. After the substepping loop, the Time resource is always set to Time<Virtual>. However, the PhysicsSchedule is still running. This means that systems running after substeps but before the end of the physics schedule will have a variable Time.
2. After the PhysicsSchedule, Time is set to Time<Virtual>. This means that if physics is run in FixedUpdate, the fixed timestep will be overwritten by Time<Virtual>.

Solution

1. Set Time to Time<Physics> instead. The physics schedule will later set it to the default clock.
2. Set Time to the clock that was used before the PhysicsSchedule.