Many sub 50 rep users have complained about the problem of not being able to comment under the limit. I am one of them. A small sample of these complaints can be found here, here, and here.
As evidenced by many of the answers to those questions, the problem that this limit is trying to solve is that of spam.
The justification is simple: we don't want the site to be flooded by comments from passers-by. ЯegDwight
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