It all depends on why the tranny was replaced.
All manufacturers turn out a bad component every now and then. If this is why the trans was replaced, I wouldn't worry about. Going by what I've been reading, the 6MT is a pretty good transmission - a least in a DD. A lot of problems with the CSC but that's not a replace-the-whole-transmission type of problem.
On the other hand, if the tranny failed due to abuse, that would lead me to believe that the rest of the car was mistreated.
YMMV
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