scripts: runners: nrf: Do not force-flush until the end

In order to better support the ability of the upcoming nrfutil runner to
defer all operations and execute them all at once, defer flushing right
until the end, when everything has been queued up (recover, program and
reset) instead of forcing execution at the program stage.

Signed-off-by: Carles Cufi <carles.cufi@nordicsemi.no>