if you run 5% faster than you did at the previous week's L2 don't you think you should get more points for you better run?
...shows how you confuse statistics with "deserving". If I did run 5% faster, I'd finish a lot higher. But even in your fantasy world where everyone takes it easy round the L2 courses, finishing halfway when everyone is trying would provide no evidence that I'm a better orienteer than someone who finishes halfway when everyone isn't trying.
(did you ever see Colin Dickson not trying? - me neither. Do I believe one of his top 20% of performances would be good enough to win the British on home territory? - of course).
Normal people won't want to read the next bit...
Most of your other misapprehensions involve the idea of "standard error on the mean": fewer people on the course means the uncertainty in the accuracy of the ranking is higher. In short, you're more likely to get a weird score (high or low) in a small event.
If you then only look at the high scores, you get an apparent bias to small events. If you look at all scores, it should even out. I already explained the right way to fix this up.
The standard error on the variance is worse, which is why they don't use it for small courses.
andypat makes the right point - it depends what you want from the ranking system.
You can include night events, or L1 weightings or anything else if your intention is to increase participation at particular events. Just don't pretend it makes the list more accurate.
The WP knows this. They have a secret list which is (in their opinion) the best statistics - i.e. based on all events. The published list is based on your best six. And for good reason - it means no matter how badly you run, however much evidence of your own incompetence you provide, your ranking score wont go down as a consequence of going to an event - the ranking list is an incentive scheme, not an exercise in statistics.
And in my opinion, that's what it should be.