twister: fix the hanging up on an exception happens during west flash

Fix the missing logic of setting the flash_error flag when
caught the exceptions. And we should let the serial thread
can be run first if flash error. Otherwise the twister will
hang up while an exception happens on closing serial, after
the #47820 got merged. This mostly happens on frdm_k64f.

Fixes #49086

Signed-off-by: Enjia Mai <enjia.mai@intel.com>