I like to make the base just a small bit longer than the model (sparred models, the base is just longer, and wider than the sparred dimension), and having about the same width to length ratio as the model. This way, when the model, on its base, is placed inside a case, there is clearance on all sides. In most cases, I have at least two bolts from under the base, into the keel, or a nut above the keel, to hold the model to the base. In almost every case, I have the model resting on keel blocks, and hull blocks, for secure support.
www.railimages.com/gallery/peterjuengst/aal shows
Wanderer on a base. My avatar shows a 1/96 scale
America on its base, and in a custom built case.