Fix physics tick counter

[rburing]

The counter is now incremented at the start of a physics tick rather than the end.

• Fixes Physics tick counter is incorrect within frame #92903

This is a port of

• [3.x] Fix physics tick counter #92941

to the master branch.

In the navigation agents update_frame_id is actually unused, unlike in 3.x (why?), so it could also be removed.

[rburing]

The navigation agents' update_frame_id was made unused in #69988, so I guess it can be removed. cc @smix8

[Calinou]

Tested locally on the 2D platformer demo (with interpolation enabled at 10 ticks per second), it works as expected.

[akien-mga]

Thanks!