I run into this with Vista SP1 DVD, and now with Windows 7 beta DVD.
What I do is install pre-SP1 on one drive, then use that to install the others from inside Windows.
When that screen option comes up for me, I've already installed the base OS and don't need the DVD anymore and just eject the DVD.
And yes, with Mac Pro and Vista, just pull your OS X drive and leave the drive you want to install Vista on and format from there.
The older Mac Pro has EFI32, newer model has EFI64 (UEFI 2.x). And Apple doesn't officially support 64-bit Vista on my system. Official support for EFI was part of Vista SP1+ from Intel and Microsoft "EFI Group" of which Apple belongs.
It should be possible to edit the DVD but my bookmark/site is not bringing it up.
Search "Prompt Vista x64 DVD ISO" has some links I want to pursue later...
http://www.ezbsystems.com/ultraiso/