Bro, I don't fully understand your question about removing the bottom or the root ball... Here's one opinion...
When you transplant, you want to accomplish several things and the foremost is to reduce stress to the plant. To effectively transplant you must completely remove the root system from it's container, and get it gently into the new medium. So, cut the bottom, the sides, or just slip the root ball out but et it out of the container. If you are able to do so without disturbing the root structure, then gently run your finger up and down on the sides of the root ball, going about 1/4 to 1/2 inch deep. Then carefully plant it in the next size container. This process gently breaks outer capillary roots which will stimulate new growth into the new medium provided. If you must disturb the root ball to get it out of it's current container, simply plant it into the next container as the disruption to the root ball will also stimulate new growth.