Well, snail is only one potential scenario. There may be others that I just can't dream up right now.
I have no experience with your model of skimmer but the needlewheels I've played around with before, some have been worse than others for the occasional berserkness that causes them to overflow. The Bubble Magus is for some reason one of the worst this way for me, but I had a CSS65 on a 20g before that was just as bad and had I run that thing as hang-on as it was intended I would have emptied the sump several times. I don't know what the cause is whether it's something in the livestock taking a mondo poop or maybe a snail spawn or who knows, but it's something. But I had other skimmers that didn't do that (ASM) so .. yeah, who knows.
Instead of weighing down the bottle so it sits under the water level, you could just make a little eggcrate or acrylic (or glass) shelf that the bottle could sit on. The bottle needn't sit in the sump per se, it just needs to overflow into the sump.
It's sort of a balancing act though, if you have to tip your bottle sideways to maneuver it out of the sump then you might still be better off having it sit on the outside of the sump on a little shelf and just with a little hose that drains back to the sump.