I would only put them in the baggie in the packaging, if the packaging listed the volume (it doesn't so this is all moot). But from the packages I have purchased, they wouldn't fit into the baggie like that. So I would have to take them out. But then we're stuck with the volume not being listed, even if you found a brand that listed the ounces on the packaging. I have never tried to put any of my glowsticks into a 311 baggie, but I bet that even if you got them in just fine, rustling around in your carryon bag would crack them and start the chemical reaction early. Of course, if they made the packaging small enough to go in the baggie it would be fine.
But I've still never seen packaging for them that gives the ounces of liquid.
So we check them.