the ones I've seen have said the Trophy goes to the main nett score only, so if you shot lowest scratch which was also best nett they would award you the trophy, no choice, only you would know you had best scratchFor Open comps, I believe Scratch should be the emphasis, so more for that, with a secondary prize for best nett.
For club comps, the pool was always self-funding, so whatever the competitors decide works - normally only a low percentage opt for the scratch prize, but the winner there often picks up nett prize as well (if they enter).
It's not the prize that matters to me anyway!