If there is a flaw in your reasoning, I think it’s covered in that first link to that Australian site.
“4. Air density
Thick, dense air damps oscillations and delays the onset of flutter. It’s like oil in the shock-absorbers of your car. Obviously you have direct control over the density of the air in which you fly. High altitudes and hot temps mean less damping and a greater chance of flutter.”
Since you used the reducto ad absurdum of outer space, try the other direction - if you submerged your plane and tried to push it through water, I think you’d see the damping effect of the thicker medium, which would make flutter very unlikely.
That goes back to what was in the Pipestrel manual; that IAS is a good indicator below 13,100ft (the number they used) and above that one should use TAS. I can certainly buy the idea that there is some threshold air density below which oscillations are inadequately damped to use IAS as a reliable measure. If that is the case, and the aircraft is capable of flight above that critical altitude, then I think the manufacturers whould be making that crystal clear in their POH. My CTSW has a Vne by the POH of 145KIAS, and there is no mention of of an altitude limit on using that number. The POH lists the service ceiling for the CTSW as 14,000ft and change.
So I'm perfectly willing to concede that at higher altitudes the Vne listed in IAS might not work very well. I don't fly at those altitudes, so at least for me I think using the listed Vne in IAS is fine...but it's certainly something I will keep in the back of my mind when flying at 9500ft or higher to clear terrain.