I have cut bottle size glass tubing with several methods. Bottles tend to have heavier glass walls and so are more difficult to get to work. The most usable results came when I used a wet saw to cut. You can rent the saw like ones used for cutting tile. I have also scored the glass with a cutter and then tap the glass from the inside of the bottle to get the score to run around. The results are less consistant. Instead of tapping, I have also taken a rod of glass, melted the end in a torch (carefully) and touched the molten glass to the bottle. The heat difference (thermal shock) causes rapid expansion and cracking. Pieces of glass can go flying with any of the methods so you MUST BE CAREFUL!
I have a Janome also and the instruction book that came with the machine shows to move the needle over when using the 1/4" foot. I used a ruler to measure and wrote down the number(4.0) It has a breakdown of adjustments that need to be made for using each foot.
I use contact paper as a resist unless I'm trying to get dimension into the glass. I haven't used the "canned" blaster but I would be careful about not getting too close to the object. I don't think there is any way to regulate the pressure from the can, but if you pull further back the pressure will lessen the chance of blasting off the stencil.
Large areas of chemical etching are difficult to acheive without streaks. I switch to sandblasting if the area is more open in the design. Also make sure to use alcohol on the glass before applying the resist. Hand oils will also cause problems.
Besides keeping the glass and bit cooler, the water will also keep the glass dust from flying. The dust embeds in your lungs. Over time it can build up causing a condition similar to miner's Black lung. It is the same reason there is water in glass grinders and tile cutters.
I am available for some questions. I have done mostly torch work (lampworking) in borosilicate and Morretti crystal. I have also worked with neon tubing. You may find that the courses the U offers are "glory hole" blowing where they melt large crucibles of glass and gather it on the end of a tube (punty) to blow into. I have very little hands-on experience there but have watched and read on it. I hope I can help.
When I have a more intricate design, I go to the local sign shop that does vinyl letters and such with a vectorized file and have them cut it on their plotter. I have gotten my local shop to cut the vinyl backing instead of the vinyl so I have a reusable stiff stencil made from the release paper instead of the vinyl. It lasts longer too. It might be able to be applied like freezer paper. I've never tried that tho. I've used temporary stencil spray to stick them down.