Yes, just set the BitZero on the surface where the stock will go and set zero for Z there, then do X and Y after relative to the stock, or, set the BitZero near the stock on the surface of the MDF and set zero for Z off to one side.
You can then check by jogging to the surface of the stock once secured and checking the Z-axis height — it should be roughly the same as the Stock Thickness for the source file.
If you have always used top here is a caution about quick actions in jog. If you use the Z+6MM to check your Z height when using top of material you are safe. If you use Z+6MM over the material when using bottom of material unless the material is less than 6MM you will crash into your project. Be sure to jog off the material before using the Z+6MM if your material is more than 6MM.
I use bottom of material for 95% of my work. I replaced my spoilboard last July 2025 and there is hardly a mark on it. I have used my machine extensively. I measure my material carefully and enter that into CC. However I use painters tape and super glue for most projects. That slight lift helps not cut through the material in scar up my spoilboard. The top of material works fine but either I cut through or left an onion skin I had to remove.
If you want a double sided tape specifically for woodworking check out XFasten. I found carpet tape not sufficient. This stuff really works well but make sure to set your Z height with the tape in mind, you want to minimize cutting into the tape as it will gum up your bit.
I put a small piece of the tape on the pool board with the backing still on and facing up. Then I zero against that.