The issues we face having a multi machine! Good problems though.
Here is what I say, since it sounds like you are going to kind of do thing sequentially. Build it just a bit taller than your tallest part to be printed since you know what you are making. Then you will have a printer, and can make the MPCNC shorter if you need to. If you make my thhingiverse printer I am pretty sure the tallest part is 2.75″. If that is the case I think you would be great to leave it at a 3-5″ Z. Most bits won’t let you cut more than about 1.5″ max so the rest is just for material clearance.
I don’t think you will need the midspan supports but they can’t hurt.
As for those foam panels, one of our uses has been pretty successful with a tattoo style needle cutter. https://www.google.com/search?q=mpcnc+foam+cutter&ie=utf-8&oe=utf-8