The typical problem with the water bottle type carboys as primary fermenters FOR BEER is that they typically come in a 5 gallon size, so there is 0% headspace for the krausen to expand, which will make a mess. Even with a blowoff tube, you really need at least 1-1.5 gallons of headroom in a primary fermenter.
A 5 gallon Poland Springs bottle would make a great secondary fermenter, if you need one.
For CIDER, there is not as much expansion in the primary and you are typically more flexible in the batch size, so using those water bottles for cider fermentation is pretty ideal. Just leave about 1/2 gallon of headspace, and you're golden!
