I mainly use the bottom of stock. This keeps me from cutting through the material into my spoilboard.
There are a few things you must keep in mind when using the bottom of material. The primary one for me in the beginning was when do rapid positions for X and Y and then Z+6mm. When using the bottom you must move the router off the material to do the Z+6mm or you will crash into your material. That was an issue at the beginning but now not so much. I just got used to the work flow. Another issue is not exclusive to the bottom but your stock measurement must be accurate. The stock thickness must be accurate or your first cuts will either be air cuts or deeper than you intended.
As @WillAdams said above Carbide Create takes the stock thickness into consideration for retracts.
So for me the bottom of material is very useful but not the only thing in my toolbox. So for some things I still use top of material.
Another useful thing by using bottom of material is I typically use the center as my origin so that eliminated the using the corner to set X Y and Z. I typically use a vee bit to set my center origin and then move off the material to set the Z on the spoilboard. The thing is just getting a workflow you are comfortable with.
If you use bottom just remember that and switching from top to bottom and back on different projects takes concentration when setting up. So if necessary start up Carbide Create and review the file before starting the cutting on the Shapeoko.
I typically use the bottom front left of the stock. Why? Most of the parts I’m making require a full cut-out through the stock at some point, so I want to know exactly how far to cut through. If the material is a thou out here and there it’s the top that will be out rather than it not cutting through or cutting through too far.
I use the left front corner because I have a corner stop on the CNC bed that I can just butt things up against and know I’m in the right place.
The only time I’ll use the top us when V-Carving or something similar that really needs to be based of the top and not the bottom.
We’re each different and there is no right or wrong answer here - if there were that would be the only option in the software!