This is one of those questions (like mast rake) where there are many different answers. All of them are probably true to some degree. I think the predominant factor is explained well by Mitch Booth in his Hobie Tiger tuning guide.

“Most boats sail with some weather helm on the rudders and subsequently you have to pull on the tiller slightly to keep the boat in a straight line going up wind. This means that you could have a few degrees of turn on the leeward rudder that is fully loaded, however the windward rudder that has very little load will only cause drag if it’s not in line with the windward centerboard.”

The way I think about it is a little different but not much. When you heal up the windward rudder has a reduced aspect ratio and becomes much less efficient as a lifting foil. For that reason you want to align it in the direction that the boat is traveling to reduce the drag. This is probably why people lift the windward rudder.

Transfer this logic to a Hobie 16 that has lots of weather helm and sideslips more than most boats and you can understand why we sail with so much-toe in.