I agree, it'd be nice to have penalties than aren't all or nothing. On the other hand, is there much of a difference between a DQ and adding 5 or 10s to someone's time? Plus, keeping track of results becomes more complicated - "was that 2:05 with or without a penalty?".
For good teams, picking up a penalty in prelims is only going to change which final heat they end up in, unless the penalty carries over. And if it does carry over to finals, and your A team is carrying a penalty, you can still play the alternate game and move the pushers to your un-penalized B team. I think this is actually worse, because now the 11th fastest team doesn't get into finals, and your B team pushers take one for the team.
Breaking the 5-second rule doesn't have much excuse - you know when you have to be ready, and if you want to wait right to the limit because you think that gives you an advantage, then you better be certain you're not going to wait too long. The Derby folks's lazy approach was kind of surprising to me - their margins of victory are tiny compared to buggy, and yet they are unconcerned about leaving their wheels on the ground for ages. Then again, I wouldn't want to carry a 200lb car all the time.
I can understand messing up transitions in the excitement of the day - 1s penalty for every foot the transition is late? Same thing for how far over the drop test line you go?
I liked the false-start rule speedskating used to have - instead of getting DQ'd, you have to start from the penalty start line, so your race is 6' longer.