I seriously disagree there, to the extent that I am reading "re-design" as "tweak".
I'd much rather tweak a game built with flexibility or a toolkit approach in mind than one built for a single play experience. Elsewise it becomes too much effort to build the gaming experience I want.
But, as this is all related to game balance, tweaking is a thousand times easier in a balanced system than in an unbalanced one. It is ridiculously easy to unbalance a balanced system to produce a particular effect. Case in point:
You want Tolkienesque elves that are just "better" than everyone else. Ok, 4e out of the box (and 3e as well) doesn't do that. So, how can it be done? Well, all elves start with a 35 point buy (in either edition) while everyone else starts with 22 or 25 (depending on 4e or 3e respectively).
There, done. Elves are better.
Now, you want to remove the "elves are better" in AD&D. How? You could whack on higher level restrictions I suppose, but, that would result in elves never being played, or campaigns ending before the hard limit is reached. You could strip out all the benefits of being an elf, but, then, now he's just a skinny human. You could increase the level limits of all the other races and give bonuses to humans, but, now you have to balance all those changes against each other, since all we want to do is make elves equal, not another race better than everyone else. On and on.
Move away from D&D to an even more imbalanced game like RIFTS and the problem gets even more difficult to solve. Because you lack any real baselines to work from, monkeying with the mechanics becomes a trial and error process. That's great for those that want to, but, unless you get lucky the first time around, you're in for a fair bit of work to sort out all the issues before you get something that works.
DIY games are fine. I disagree with the idea that they are somehow "better" than out of the box games, but, that's a personal taste issue. I have zero interest in futzing about with mechanics. I just want to play the game, focus on the game and not worry about whether or not this or that rule will work today. I just want the mechanics to sit in the background and come out when needed, with a tool that will work well enough right now. It doesn't have to be perfect, I'm more than willing to accept that. But, it has to work.
In my not so humble opinion balanced systems are robust. Imbalanced systems aren't. I prefer robust systems.