It's only tall trees, it's hardly a classic :-)
In all seriousness, together with the messed up fades on I walk away and together alone, it does feel like the main albums were prepared pretty carelessly. It would only take a person reasonably familiar with the albums to give them a listen through prior to them being sent off to be manufactured.
I've always liked Tall Trees. But, why do you assume the lack of fade outs on those other tracks is a mistake? Fades are a decision made during the mastering process, and being that the albums were remastered, apparently a different decision was made this time around. I think it's consistent with the "peek behind the curtain" offered by the bonus discs. I don't think it's a mistake, unlike the Tall Trees thing.