I think D2 will depend on wherever your chosen comp ends up and I remember reading on here that it does not matter really as the comp chamber is sealed off from the mid driver chamber. D1 will probably also end up being wherever you think it looks right depending on which comp horn you get for your chosen driver.
Yeah the space behind the comp driver should not matter. If you were using a different mid range cone, you might be able to utilize the D2 space to increase the chamber volume up to like 3 times the volume in the plans. Would certainly change the response and spl, but it would be an easy way to work with alternate drivers requiring a larger chamber volume.