esp32/machine_timer: Reuse Timer handles, deallocate only on soft-reset.

The patch solves the problem where multiple Timer objects (e.g. multiple
Timer(0) instances) could initialise multiple handles to the same internal
timer.  The list of timers is now maintained not for "active" timers (where
init is called), but for all timers created.  The timers are only removed
from the list of timers on soft-reset (machine_timer_deinit_all).

Fixes #4078.