Between PitchFX and Trackman, MLB teams have spin, velocity and trajectory data for every pitch in the MLB and most AAA parks. Vegas included. Now tell me exactly how with that information in hand we can't measure the flattening of a pitch in altitude.
As for your 2nd point, the game theory changes are indeed probably the biggest effect. But their overall impact is reflected in the park factors. Yes, more fastballs get thrown, yes hitters know that, yes it makes it easier for them to predict what's coming but the net effect is easily measured by the outputs over many years of data.