Thanks for your always detailed feedback.
First, I don't think it is fair of you to be in the shoes of a new player as you have manipulated level mechanic in a previous title. They are an advanced mechanic, purely optionnal for the whole chapter. At first I had turned it off for the chapter but decided to go with it.
Basically, the focus on numbers has disrupted your discovery unfortunately. I will try to think of a way to take that into account for players in a similar case.
This game will not be a tight puzzler where mechanics grow together. It is overwhelming by design.
I will include your suggestion for 1up, and level3 flag is definitely a bug or rather a hole in design. How score works will be explored in a future chapter (if I do complete another).