Being a bit more serious, if it were me I would probably wait for the small run ED mentioned to test out the mass production. Unless I am making that up, or misunderstanding what he said. If you can still get it early and have all the hardware updates, do that. While it is cool that you could get prototype hardware, I think it might be better to have the whole shebang.
A few reasons for this suggestion are based on how active you are here. If you are helping someone else troubleshoot, it is better to have the same hardware revision. The same forr someone helping you solve a problem. Additionally, if you ever decide to do any serious hardware hacking then you might want to have the same thing as everyone else. I doubt it would matter much, but if others try to follow your lead, or you theirs, you should be looking at the same thing as everyone else. Due to how minor the changes are it really probably won't matter for troubleshooting or modding, but it might.
From the software side of things, I can tell you that it really sucks when
@ptitSeb releases a port that doesn't work as well, or at all, on my CC Pandora. I was so happy he was working on Eldritch, yet I can't play it on my Pandora. I know that is a totally different issue, but it just makes me think. Although it may not be a problem, are you willing to risk losing out on software and games due to eMMC and RAM (yes, we have had many discussions about this, and you don't mind, and possibly prefer, 2GB). Even if that situation never arises, you could still be disadvantaged compared to most Pyrates (is this a term we all agree on? if not, I mean Pyra owners/users).
Regarding the display, if that is a problem I am sure ED will sell you one of the new ones, and you will always have a spare. You could also eventually build a whole second unit if an upgrade for the CPU board ever comes (you mentioned getting extra cases, so make a case, get an extra main board and keymat, add the "bad" display and the OMAP5 board...maybe a display board, I guess).
Ultimately, you paid more, so will it be more valuable to you as a prototype, or would you rather have what everyone else has?