When you lag, it does not affect your in game velocity. As such, a game can lag to high hell and show you falling like a feather, but hit the ground like a truck. I know that to some it might be hard to understand that there is a lot more going on in the model that what you are being shown, but there is a value tracking your current velocity, as well as one for your location and acceleration, that are independent of the user interface, and only updates on game refresh, rather then a internal timer. Using a plot point for maximum velocity achieved will not solve any problems to do with logic and lag.
If the game lags and takes too long to refresh, it has to calculate a much larger part of the trajectory of any moving object between game cycles. The longer the lag, the more flaws creep in.
If an object moves at 1 pixel per millisecond towards a 1-pixel wall 10 pixels away, and the game lags 20 milliseconds, the object will be behind the wall on the next cycle. Most physics engines pick this up, of course, but at higher lags in situations with a lot of awkward corners, high speeds and platformer-style physics, things get weird quickly.
Whether this is the reason for the fall damage glitches in the first place doesn't matter, since the current glitch where cloud bottles don't stop fall damage is only possible if there is a variable tracking either your total fall distance or maximum fall speed.
Edit: Total fall distance. Falling from my base all the way down to hell did about 7700 damage, smashing into a ledge halfway down cost me only 2800hp.