Pretty Print isn't gone. It's just not automatically done any more. Use Tools->Reformat Html->Mend/Mend + Prettify (also available from the Code View context menu) whenever you want to reformat/mend your code.
No version of Sigil that I know of changed the 1999 namespace to a 1998 one (and if the old htmltidy pretty-print ever "fixed" anything, I assure you it was entirely by accident.
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I don't believe you need the namespace in the span since that namespace is always added to the html tag.
I'll look into old vs new behavior, though.