There's no such thing as "waterproof". There are various degree of water resistant varying from drip proof to high pressure water spray. See: The first digit after the IP is the degree of protection against solids. The 2nd digit is the degree of protection against water. You'll need to define what level of protection your unspecified device requires.
Sure. However, if you overcharge any battery, it will get hot and produce gasses. These gasses are often caustic and will rot your electronics. Therefore, a separate battery compartment is advised.
LiPo batteries are also subject to bulging (inflating with gases) when charging normally. This is normal and probably can't be totally eliminated. You'll need some expansion space to handle the bulging.
No, or rather it's a question of how much out gassing and bulging you can tolerate. If you belching hydrogen gas from a wet cell, you could easily create an explosion if there's oxygen present. Better to have a controlled exit path for the gasses, than to use an air tight seal and have the gasses accumulate.
You might be amused at a GPS receiver package problem. The battery gassing problem was recognized early and a small hole was left in the package to take care of any out gassing. The hole was deemed small enough not to present a water incursion problem. I suggested otherwise, but was ignored. This GPS receive was for sports use, which included kayaking. The unit was normally left in a warm place, and then splashed with cold water. It was then warmed up for a while, and again immersed. When hot, the air inside the GPS would expand and leak out through the tiny hole. When cooled by the cold water, the air would contract, and suck in whatever it could through the tiny hole. Usually that was a tiny amount of water. Repeated many times during a river trip, the GPS receivers started showing noticeable and permanent condensation on the inside of the LCD display. I pointed the project engineer to the hard disk drive industry, which had a similar problem with package pressure equalization on their drives, and solved it with various air-permeable and water-resistance membranes. When you say "sealed" I think of this problem, which hopeful you will not repeat.
Jeff Liebermann email@example.com
150 Felker St #D http://www.LearnByDestroying.com
A friend modified an old Garmin to truly seal the package. He took a flight and all the keys were depressed due to the air pressure change. Some of these planes only pressurize to an equivalent of 8000ft.
Ammo cans can create quite a vacuum if you road trip goes from sea level to the Sierras.