The above referenced article is one of the most confusing and misleading things I have ever read. A lot of it concerns the danger of high altitude cruising with turbocharged engines, and the resulting high TAS. But even normal-engined RVs can climb quite high (the 10 to over 20,000'), and then descend at very high speed. So this issue is not restricted to turbocharged aircraft. The correct answer is (C), neither of the above. There are many different flutter modes, and their threshold of onset depends, in general, on the parameters rho (density) and V (true airspeed). Many of the most important modes on typical single engine airplanes have thresholds where these variables can be combined into the form rho V squared and nothing else. Since this is the definition of indicated airspeed, for these modes Vne can be expressed as an indicated airspeed (only). But for other modes, life is not so simple, and the threshold depends on rho and V in an algebraic expression which is different from rho V squared. For these modes you need to specify, for each rho, a V. But since you have specified rho and V you can calculate IAS, and specify an IAS for each rho (rho usually being changed into an altitude). But it incorrect to say you can specify Vne in terms of either TAS or IAS. It also depends on altitude (rho).
One of the most important modes that does not scale as rho V squared is where the wings flap like a bird (along with a torsional twisting 90 degrees out of phase with the flapping). Aircraft like gliders, with long, flexible wings, are most suceptible to this mode. Most single engine airplanes have relatively stiff wings and do not easily excite this mode.
Certified aircraft must be able to specify a Vne in IAS, good from the service ceiling to sea level; or, placard the plane with altitude/airpeed limits if they cannot comply with a single IAS number. (see FAR part 23). Most normally certified aircraft, even high ceiling turbocharged ones, can get by with the single IAS for Vne. So what is the story for RV's? Since RV construction is similar to Piper's, one might reasonably assume that a single IAS will suffice for Vne. But absent testing, no one can say for sure. This is the price we pay for flying EAB aircrft.