Firefox and multiple firefox profiles isolate cookie storage and I also use Fluid on OS X to build site-specific browsers. The paid version offers a feature to isolate cookie storage within each app.
If that's true then it's utterly insane. This StackOverflow question from 2008 seems to confirm what you're saying, though:
http://stackoverflow.com/questions/364219/how-can-i-have-mul...
I really hope it isn't still the case...
Where are you getting this? Safari and Chrome (both built on webkit) definitely do not share cookie stores on OS X.
The easiest way to test this is with Safari and any of the OS X site-specific browser or http debugging tools.
I think you're referring to other applications which embed Safari's rendering engine. I wouldn't really call those browsers.
New browser feature - open this site in a temp VM.
I would encourage browsers that support isolated profiles, multiple browsers that don't share cookie storage, or using a jailed site-specific browser approach.