Everything that you said about Indicated versus True Airspeed is correct. However, generally the Vne that is given in the POH, or Owner's Manual, or Dash 1 (military jets) will be given in INDICATED AIRSPEED, because the companies that build the aircraft know that this is what the pilot has easiest access too in flight.
Actually, indicated airspeed (or more accurately CALIBRATED airspeed which is just Indicated +/- installation error) is useful for expressing airspeed limits on airplanes, because indicated airspeed sort of expresses the amount of force caused by the velocity of the air.
Let me see if I can explain why: You are correct that indicated airspeed measures the force of the air molecules moving into the pitot tube, so the more molecules there are, the more force there is. Or the faster those molecules are moving, the more force there is. If you were looking at TRUE airspeed, then you would be looking at the speed of the molecules across the wing, but the forces generated by those molecules at a given TRUE airspeed would depend on the number of molecules. Or in other words, the forces would depend on the density of the air, in addition to the true airspeed. But that's basically what the indicated (calibrated, really) is all about.
Now some aircraft also have some maximum airspeeds that depend on Mach effects as well as the actual forces on the surface of the airplane. In those airplanes, generally the barber pole at sea level will be at the maximum indicated airspeed, but as the altitude increases the barber pole will move down to show the maximum Mach number limit. I have know idea what the exact gizmo is that does this, but the idea is that it should display the correct limiting airspeed even if the mach number is what is causing the limit.
The other way that it can be displayed is with seperate airspeed indicators and mach indicators, where you'd have a limit for each, such as "316 IAS, or .67 Mach, whichever occurs first". Incidently, this is the T-6 limit. (Although, the T-6 uses an airspeed indicator where the barber pole moves automatically at higher altitudes, rather than a separate mach meter).
Anyways, like always, read the POH for YOUR airplane, and see what it says. Where it lists the Vne it should also tell you if that is indicated, calibrated, equivalent or true. If all that it mentions is an indicated limit, and doesn't mention any notes or warnings about altitude corrections, or temperature corrections, or a seperate mach limitation or whatever, then that's really all you should need to worry about. The manufacturer should have done all of the thinking about true vs. indicated vs. mach vs. equivalent vs. calibrated for you.
