I think if it's a good idea depends on how you plan to carry it.
If you did something like use a Nalgene-sized pipe and carried it in a MAxpedition Roly-poly with a Nalgene/Guyot in another Roly-poly, you could clip them together and ptu s sling strap on it for a handy little kit.
However, if you're going to carry it in say, a Maxpedition Jumbo, then it'd be better to have a water bottle int eh bottle carrier section, and your kit in flat boxes that fit the other compartments.
I don't like the kits in a bottle idea, because where do I keep the kit when I have the bottle full of water? If you have another bag or something to carry the kit in when the bottle is in use, why not just plan to carry the kit that way and leave the bottle empty?