Count me among the grumpy dinosaurs if you wish, but I'll sit out this event. Penpa is fairly good for what it is, but it's still very far from solving on paper from a user experience perspective. It probably took me a while to learn when I was a little kid, but by now I'm quite adept at using paper and pencil, and that is a very very high bar for any kind of user interface to compete against (largely because of another equally amazing piece of technology: the eraser). Penpa has a learning curve, not an unreasonably steep one from what I can tell, but for me it just kills the enjoyment of the puzzle to not be able to just draw harder/lighter lines by pressing harder/less hard on my screen, and quickly erase the lighter lines. (I'm sure there are features to do something equivalent, but they require navigating a user interface.)
Also, on the second practice puzzle, Penpa let me put stuff into the grayed area and it wasn't clear (until I counted and convinced myself it couldn't be) whether that region was meant to be part of the puzzle or not. (I guess that's why there are practice puzzles at the start, so people who will be doing this seriously can figure out how to live with Penpa.)
The first part is a personal preference issue which we can't do much about. As you said, there are ways to do whatever you mentioned (I even noted two possible ways in my introduction post) but I agree it can be difficult for someone who is used to paper solving, and I can sympathize. Overall though, since there are so many contests that are catering to either only-paper solving or allow a mix of both, its nice to have an only-online one once in a while, allowing for the fact that it may not be for some players.
The second part, you aren't the first one, and I will again direct you and others to my introduction post as well as the "About" link at the top of the contest page where we have divulged as many details about the rules, visual clarifications, penpa clarifications, etc. as we can. At some point I think its fair for us to expect that people will read the information we are putting out, or at least, expect surprises if not.