As I take the time to clear rocks and trees I'm trying to space plan. I'm also curious if upgrading from a small to a large habitat causes it to change size. Do all habitats take up the same amount of X-Y map space?
No they don't; Large Habitats take up more space (usually 1 block wider and longer) and some elemental habitats are larger than others. When you try to upgrade a habitat you'll have a chance to move the habitat and you'll see it's new dimensions to allow you to move it to where you have space.
Large Earth habitats are the largest and Plant habitats are the smallest I believe. Rainbow Dragon habitats are actually even smaller but they're a special exception.