Hi Wreavant!
I don’t have an answer for your first question, because I never had a situation where the subdecks have different options groups than the parent deck, but I should be able to clear your second concern:
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Switching the scheduler will reset all your learning cards (the red ones), but it will not reset anything else. Your review data will be kept, only learning cards will be reset.
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If you feel insecure about switching, consider that Anki creates backups whenever you exit the Application. You can always restore your collection if you don’t like the changes.
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Studying from a parent deck will not mix new cards (sadly), it will only mix review cards.
(Subdecks - New cards Randomize)
I have been using the 2.1 scheduler for almost a year, main reason being that it allows for a longer, more fine-tuned learning phase (more steps) with its introduction of the “hard” button for learning cards.
I see no reason why it shouldn’t be the default scheduler by now.