I’ve seen it done both ways so both should really be supported. Here’s the Boosey & Hawkes engraving of Arabella by Strauss, pg 91 where Piccolo (played by Flute 3) is under Flutes 1&2:
FWIW, Finale doesn’t support this natively, but you can reorder staves using TGTools/Layout/Staff List Manager, so you can change this on a system by system basis if you want. It would be cool if Dorico had a similar feature.