I interpret The Bitter Lesson as suggesting that you should be selecting methods that do not need all that data (in many domains, we don't know those methods yet).
The Bitter Lesson is saying, if you're going to use human knowledge, be aware that your solution is temporary. It's not wrong. And it's not wrong to use human knowledge to solve your "today" problem.
System prompts enable changing the model behavior with a simple code change. Without system prompts, changing the behavior would require some level of retraining. So they are quite practical and aren't going anywhere.