Not exactly. The W3C spec stated the box model should work one way and everyone but Microsoft/IE did it that way. This is a new part of the spec which didn't exist back then.
However, since IE had 95% market share, everyone marked up their site according to Microsoft's model instead of the W3C. It's affectionately called "quirks mode" and really screwed people up, remnants of which I still see today.
MS thought the spec was wrong and the W3C actually intended the more logical model, thus following that assumption when they implemented IE; and why the W3C didn't change the spec, or why other browsers didn't follow, is I think more of a political issue.
Well if MS thought they had a better model, they could have proposed it to the W3C and introduced it as -ms-box-model or something. Even if IE's model were superior, it was disastrous to have two contradicting models in different browsers. Maybe whole debacle with 'quirks-mode' could have been avoided.
Many years ago, I read that Microsoft "misinterpreted" the spec but I don't recall the source.
Microsoft is a member of the W3C. I don't remember where they were then but, today, they are listed as contributors to writing of the spec and I'd assume they were then, too.
The box model has not changed and your statement calling this CSS box model property "more logical" is an opinion. My opinion, as well as many others, is there is nothing wrong with how width/padding/border/margin works. Some complain that width should include all that but, to us, it's perfectly logical the way it is.
This new property is only a different way to set the same thing but, again, the model has not changed in any way.
However, since IE had 95% market share, everyone marked up their site according to Microsoft's model instead of the W3C. It's affectionately called "quirks mode" and really screwed people up, remnants of which I still see today.