it's irrelevant weather the bottle is above or below the bleeder. it's more important that the hose stays submerged in the brake fluid than weather the bottle is above or below the bottle.
some people argue that it's better to have it below the bleeder. this way you can see air bubbles trapped in the line to know if the air has been pushed out. others argue that it's better above for the reason why you stated.
i say it's irrelevant. hook the bottle in the easiest way you can as long as it doesn't fall exposing air to the line that should be submerged.