Well, the fact that lag needs to be compensated for can't be eliminated, so no matter how you do it there's going to have to be some "clock manipulation" performed by chess.com. As a result, clocks appearing to not run properly is inescapable, however how you compensate for that lag can have a big impact on how it is perceived by the users.
I'd put forth the theory that this mechanism is much less likely to be noticed as often, misperceived as badly, and also much easier to understand when explained as "lag compensation", as that's exactly how the clock would respond: it would lag.
All too often, threads pop up in which a player who's opponent has had time added back to their clock as a result of lag compensation accuses people of hacking the clocks and in some way "time cheating".
It seems to me that there is a very simple fix for controlling the way lag compensation is perceived:
I believe that this would completely eliminate clock's jumping and gaining time and phantom time-outs in which an opponent's clock runs down to zero and sits before they suddenly appear to get awarded more time, and as a result much of the confusion and frustration surrounding this behaviour.