The OP originally posted a link to a tournament game, so some of the discussion here doesn't really apply, like getting your clock positive again after going negative. My general feeling was that the problem was greatly improved once tournaments had the option to prevent skipping overtime players.
There is a new wrinkle, now that some games like Heat (and Formula D that OP was playing) can continue normally after someone is skipped. It probably makes sense to immediately skip players if you somehow know they aren't coming back (or maybe they explicitly quit). On the other hand, it's better if the game completes normally, rather than reach the tournament's maximum game duration, even if some players went overtime.
In these threads, I often wish the OPs would acknowledge their role in running out of time, and that includes joining tournaments where they are not certain they can keep up. All that said, I also don't like it when someone skips someone at the last moment to avoid a loss when they could have skipped them much earlier. It's even more annoying when there was someone else whose clock was even more negative. I guess the worst situation (that didn't happen here) is when the person who does the skipping has a more negative time than the one they are skipping.
One small change that could be made is to only allow the player with the most negative time to be skipped. The suggestion is
here.