I think before we make a decision we need to think this through, by asking two questions:1. What do most users expect here, in terms of ordering? If we don't know, how can we learn what they do expect?2. If users expect the primary action to be on the right, how would this change core forms other than Preferences, such as signup, login, editing (in wikitext and VE)?
In the mean time, the simplest thing to do is not to rewrite Preferences to make a new divergent standard, but just update the button classes without mucking with the ordering. That's the minimum viable release for updating Preferences to match mw.ui styles. This will provide the most benefit with the least effort.
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