I agree, that rule should definitely be enacted for Sonic 06. Also, as far as the handling of version differences go, although I -hate- it when I'm at a disadvantages(and often find myself searching for a way to get around that disadvantage, which sometimes I'm successful in...like
here), I would say to keep things the way they are. Yes, the disadvantages can be quite...staggering at points like SA(DX)'s Final Egg, but even with disadvantages, it's not impossible to climb up the charts. For example, yoshifan is the champ of SA2(B) with only the gamecube version, while Psyknux has both versions. I'm the champ of SA(DX) with only the gamecube version, while Jawzun has both versions.
Alternatively, I would go with yoshifan's method of handling it, but there's only 1 problem I see with that which would, in my mind, create a bit of "unfairness" for some. Let's create a scenario for Final Egg: Sonic in SA(DX). We'll assume that the top 9 are dreamcast and the rest are gamecube. A newcomer, dantheman(lol), arrives and starts to compete in SA(DX) and has the dreamcast version. If you'll look at the
chart, in accordance with yoshifan's method, you'll see that the maximum points this newcomer can get is 9 points, regardless of what his time is. Let's say he knows not of the glitch, and couldn't care less about it. He runs through the stage and finishes in 3:03:xx. Now, according to yoshifan's method, if he had done this run on the gamecube version, he would receive 23 points, but since he used the dc version he'll only receive 9 points. You'll notice that SkyL finished the stage in 1:21:96, yet he'll receive 10 points for his time. Although RPG brings up a good point of how to handle that situation, what if there's a dreamcast player who could finish the stage without using the secret capsule in 58 seconds? The player should get 9 points instead of 0 just because they have a dreamcast instead of a gamecube? I do believe that the capsule is the only difference between the 2 versions, so in actuality, they take a hit solely because of the version they have(which is exactly how the current system is). I see no way possible to make competition completely fair when it comes to version differences, other than deleting every chart that involves the slightest version difference, though I hope it won't come to that. Although that would make things completely fair, it would eliminate a shitload of charts on the site, especially for SA(DX) and even more so for SA2(B).
So in conclusion, I believe that the "suck it up" concept should stay in place. Besides, the disadvantages -usually- balance each other out in the end, though not all the time. My only example, don't expect to be champion of Sonic Heroes if you only have the ps2 version. >_>