How do manufacturers/kit providers determine Vne?
$V_{ne}$ is typically set to about 90% of $V_D$, the maximum design dive speed.  This difference provides a safety margin.  Above $V_D$, damage may occur due to flutter or structural failure, or controllability considerations may make the aircraft unflyable.  The aircraft is not guaranteed to fall apart at $V_D$ due to additional structural and manufacturing margins.  

During flight test, the aircraft is flown above $V_{ne}$, up to, or close to, $V_D$.  Appropriate safety precautions are taken, e.g. parachute.  Any failure below $V_D$ indicates a design or manufacturing issue that must be resolved prior to certification.

The limitation to flight below $V_{ne}$ (as opposed to $V_D$) during regular operations provides protection against airspeed measurement errors, pilot errors and some margin against structural degradation over the lifetime of the aircraft.