Just experienced this problem for the first time. My installation is a bit different from the one described in the original post —*I am running Mountain Lion 10.8.2 and my boot drive is a 240 GB SSD, so the issues of large sizes don't seem to apply. Nevertheless, I got this error.
My fix was essentially the second option. I extracted the boot drive and used a USB-connected hard drive dock connected to my MacBook Pro. Since the drive is bootable, I reset the system into that install, and ran MultiBeast installer again with the same familiar options checked. Not sure why, but it worked. The takeaway here is that everyone should have a hard drive dock! They're relatively inexpensive, and with an eSATA connection, there is essentially no slow-down. Great for making clones and for booting in odd situations like this.
It should be noted that it is very bizarre indeed to see an installation that is normally at home on my desktop Hackintosh suddenly appear on my MacBook Pro. Surprisingly, most of everything adjusts and works like a champ.