Ok,

Firstly VNE is very much limited by TAS not IAS. If
you understand the maths behind how an ASI works then
you will know that the ASI indicates a TAS based on
an assumed air density equivalent to sea level. TAS
is the speed that affects flutter, IAS is simply a
gash estimate of TAS which is reasonable at low altitudes.
Hence the rules of thumb for safe flight at altitude.

Secondly, ground speed at altitude is much higher than
TAS due to lower air density and can be greatly affected
by very high velocity winds at altitude. This is how
high average speeds can be achieved without exceeding
TAS VNE. Try looking at your GPS groundspeed when at
high altitude, it should be much higher than your IAS
even when the wind effect is removed.