twister: pytest: fix missing messages from hardware target

When pytest harness test is run on harware, messages sent from target
right after application start-up are lost, because connection to COM
port is not established yet. It can cause unexpected
behavior of a test. Fix it by flashing and running application after
connecting to COM port when testing on hardware.

Signed-off-by: Michal Smola <michal.smola@nxp.com>