very cool concept, I ended up not putting any attention to the letters and used only the hints
Thank you so much. Yes it is indeed possible to ignore the crossword clues if you populate the puzzles with hints - effectively turning each level into a sort of shape puzzle. Though at the default difficulty when you have incomplete hints about the position of each word-train, crossword clues will typically provide useful indications about the position of a handful of words - letting you then solve for the rest.