Dude, the way I see them clones - they are like twin brothers.
Two of my buddies are twins and they both sound different. They look the same, but they sound different and I think that's because they don't live the same as the other one. They have different lifestyles.
Clones in PT were the same because they ate, drank and trained the same. They lived together in equal spaces. But Boba had a different life than clones, you don't know what Boba has been doing. For all you know he's a weed addict and his voice sound different because of that. Or he's on steroids and has his own death metal band where he is the lead singer.
Use your imagination, man. Star Wars is FANTASY. Use yours to fill up the holes the way you want to.
And also - the original voice kicks ass, but Morrison's version, on the other hand, sounds boring. He has no emotion or character in his voice (as much as I like the guy as an actor).
And even though I'm having an awesome time on the ANH:SE Redux Ideas thread, I've always thought that OT>PT.
And that's the explanation you need - OT>PT. No matter what.