It's been a while, but I don't think I had a capacity >4TB at the time.
But it is nasty as you said. I think you understand the problem, but just in case: if you do not use GPT tables, you cannot physically reach any storage beyond that 2 (or 4?) TB limit. It doesn't matter how you partition the drive (or array) - that extra space can simply not be accessed.
There may be some dirty hacks around now, but at the time it was quite an unpleasant surprise to me. Carving out a smaller virtual device for booting wasn't something I wanted to do at the time; on the upside, I learned to appreciate GRUB.