you are correct. air bubbles will rise, basic science.

why this is irrelevant is the next pump of the brake pedal 10 seconds later this air bubble will be pushed out before it has time to rise naturally to cause problems. also when you bleed like this the line is curved above the bleeder before it goes into the bottle. the air bubble will stay in the middle of the line and not go back into the bottle, also basic science. the only way it can rise back up into the caliper is if the bleeder is at the bottom of the caliper, and you don't want that.

i have bled a lot of brakes with a hose attached to the bleeder and the other end is submerged in brake fluid in a bottle. 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.