I think this is currently only supported by writing the doctype out as text:
<?xml version="1.0" encoding="utf-8"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="html" encoding="utf-8" indent="yes" />
<xsl:template match="/">
<xsl:text disable-output-escaping='yes'><!DOCTYPE html></xsl:text>
<html>
</html>
</xsl:template>
</xsl:stylesheet>
This will produce the following output:
<!DOCTYPE html>
<html>
</html>
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