Do you have experience with the automated filling systems for lip balms, like your bottle fillers?
Any bottle filler, single shot or hand held, multiple shot filler is slow compared to the trays. Until you get into a full-line conveyor/packaging/filler system, upwards of $100,000, you are better off with flood trays.
We have customers with more than 50 of our double trays. They must find this method pretty efficient.