mill bit lengths

[Jonathan]

I would think it is better to have extrusion as your gantry support as you can change or make it a bit longer and just move it up as required ??

Yes - additionally it allows you to have the minimum distance required for what you're cutting. Clearly that makes it stronger. It's a matter of how difficult it is to actually move the gantry up and down.

even adding two to three more sheets of MDF to the bed would add extra hight if you remove two for a 4 axis ??

Yes it would ... although you'd probably need more height that that for a 4th axis.