Card rooms use one deck for poker.
With two decks 5 of a kind would be harder to make than a straight flush. So I would consider them to beat all the straight flushes, including the royal. It could be debated that it should beat all the straight flushes except the royal (because it would still be harder to make exactly a royal) but that just makes things all ugly and not logically smooth.
I still play Canadian stud where small staights only beat a pair, despite the math suggesting that they should beat two pair. Consistent logical application benefits the players, even if the math isn't perfectly aligned.
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