> he testified that he didn't use this code
I read that as implying that the emails included code. As a developer, my emails have included code; and it's not so surprising that his emails would have included code when he was working with an external party.
> if it's a clean room implementation
It cannot be a clean room implementation if the same individual is involved in the creation of both instances.
As for clean room implementations, that is true, except in California.
Here, it does not really hold in court at all:
You can leave one company to join another doing more or less the same thing (because non-competition clauses are banned here), as long as you do not copy the code itself.
It sounds like you and your uncle post are both programmers trying to look at things too much from a logically moral perspective, rather than actually how the courts view these things, since you aren't very familiar with the latter.
The quote from ZeniMax in the article is "With the start of the trial of our case in Federal District Court in Dallas [...]"
Carmack lives and works in Texas. In fact I think (though I don't have a citation for it) Carmack's choice to stay in Texas is the reason Oculus has a Dallas office. Of course Oculus and Facebook headquarters are in California. ZeniMax headquarters (according to Wikipedia) are in Maryland.
That is why Samsung built an ice skating rink in front of the U.S. District Court for the Eastern District of Texas -- to lobby the judges who heavily favor patent holders -- literally thousands of patent infringement suits are filed in this particular court because of this.
I don't think it's unlikely that among the thousands of emails Carmack downloaded on his last day, that some of those which involved working with an external developer would have included such attachments.
Lots of people do this when leaving a job, even when they are not supposed to. It is your correspondence for the last X number of years, you want a personal copy.
Carmack would have a greater incentive to copy the emails since he clearly was blurring the lines between personal work and private work while working for id which was inherited by zenimax when they bought id.