Hecubus,
If you want a bottle with the cliche' look, lumpy with lots of bubbles, then hand roto casting may work, but if you want your piece to look like a real bottle, or a modern one, then you have a trickery issue to deal with.
It would help to see an image of the bottle you are trying to replicate. Perhaps instead of two halves, I would suggest (depending on the bottles shape) cutting the bottom off and making a mold with a inner core. One mold for the upper portion of the bottle and one for the bottom. This way you have a controlled volume in which to pour resin, and then you could use a pressure pot. If your bottle is mold blown (the glass was formed in a mold) then there will be a seam near the bottom you can use to hide the seam in your cast bottle.
I have roto cast, by hand, bottles for film and it is pretty hit or miss. The best results I obtained were using epoxy resin in silicone molds and I heated the mold and warmed the resin. The heating the resin lowers the viscosity, and thus traps less air. Heating the mold adds more heat to the resin and helps it cure more evenly as you slush it around in the mold. But you have to work quick, as the heat will cause the resin the set quickly. If you get lucky, you may get something acceptable on the first one or two. If you don't, you have to study the failures and try to adjust you technique accordingly.
robstyle,
Hand blown glass is typically even, and bubble free. I'm afraid the modern idea of hand blown items being bubbly and lumpy is just a result of poorly skilled novice glass blowers trying to replicate historic pieces. I have worked with hot glass and made and helped make many different types of glass and it's all even and bubble free, as well as quite thin. Even ancient Roman mold blown glass was smooth and bubble free.
I'm not sure to which bottle you refer in the pirates movie, as the hero bottles in Stranger tides were made by Historical Glassworks and were even and bubble free. Perhaps the bottles used for Blackbeard's ship collection were roto cast in resin.
Here is one of the hero bottles from Stranger Tides. The slight modeling you see in the color, is the color, not thickness. (I think this was an alternate color not chosen)