Wood craftsman kits are made from trees. In a tree the wood is to help transport water from the roots to the branches (actually to the photosynthesis factory - aka leaves). Getting one side of a wood kit wet (and water based paint has a bunch of water in it) will cause that side to absorb the water and grow causing things to warp. Best way to stop warping is to not use water based paint. Use oil base paint and you shouldn't have a problem. Extra bracing is always a good idea as some of the oil will also be absorbed, but it most likely won't warp.