The shed has a normal lock, in addition to the padlock. There's no mention of using a padlock this time. It's possible to pass things through the window, so the key could have been put back in with string.
As for Maria's death, I think she knew she was taking poison. Remember the other tests? Surely hers was similar (yours / Rosa's / everyone else's).
Rule Y is probably "While standing by the rose, Maria will receive a note. Rudolf will die at the first twilight, and Battler and Maria will survive to the last twilight."
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