You are right that there are some new users misusing the answer box to post a non-answer which is a comment (or a tiny follow - up question, which qualifies as a comment rather too), so those 'answers' gets either transferred into a comment (by moderators) or are deleted rather quickly either by voting process or by moderator action (again).
Lowering the reputation treshold for comment privilege will reduce this problem, of course, but other than 'answers' comments can't be deleted in a review queue, they must be flagged and its up to the moderators to delete them. Having a lower treshold will provoke more spam comments, most likely.
I am unsure that upvoting (new) users over the 50 reputation limit in order to allow them to leave comments everywhere is a useful strategy. If they've posted a good question/answer somewhere they will have those upvotes rather soon.
As Joseph said: The treshold value is a SE - wide limit.
Please take into account that the limit for participation in Chat is actually only at 20 reputation points, so this could be achieved easily, in my point of view. The relevant user can ask or post a comment regarding a question another answer in chat, although it's most likely not as effective as on the main site.