The bottler can be used to make bottles of honey, if you use pipes to pump the honey into the side then fill the bottler with glass bottles. It can also be used to bottle bees to upgrade your existing bees' genetics. 
The bottler used with a piston, set up as shown below, SHOW SQUISHER can squish a bee of your choosing into a bottle, killing the bee but giving you a bottle of genes that can upgrade all others in your apiary. Genes can be combined and put into honey treats [LINK TO ITEMS] to give your bee the chance of an upgrade. Bee genetics can be seen when the bee is put in a bee cage [LINK] and moused over. 
It is a bit barbaric, but this is the best way to get a pack full of super bees that are awake at all hours, immune to weather, completely passive, and wildly productive, otherwise it would lead to countless hours of selective breeding that may or may not yield results. RECIPIE