Your statement "then the latter wrestler is the winner by default, since the first wrestler has reached the 5 match limit" is not called out in the NHFS or NCAA rule books.  It is one possible interpretation of the stated (5 for NFHS, 6 for NCAA) match limit.

With regard to the pigtail match scenarios, the check box in the "File"/"Ladder/Misc preferences..." window specifically states "Force a tie after 5 competed matches (only when the bracket size is 16 w/o pigtails".

I am therefore moving this to the Suggest Enhancements section of this Forum.  Your request is to add a new feature to the program for selecting what to do when one wrestler has reached the limit when the other has not.  It further requests that the program enforce the 5 match limit for brackets with pigtail matches.  Such a request would then need to also support 8 wrestler brackets.

On page 7 of the NFHS Case Manual, this situation is presented.  However, I read your responses to an earlier post (dated Jan 2017) which stated a work-around.  This is exactly what I did.  For each "tie" in the 3rd and 5th place matches, I counted the number of matches of each wrestler (omitting any byes or forfeits).  If one wrestler had less than 5 matches, then that wrestler was declared as the winner and the result was "5-match rule" which the program changed to read as "5-0 match rule".  If both wrestlers had 5 matches, then the result was left as a "tie".  However, both wrestlers were specified as 3rd place or 5th place winners, where both wrestlers are presumed to receive additional points.  According to the Case Manual, both wrestlers should be awarded 4th or 5th place, and receive no additional points.
     I can do the manual count to determine the winner by the 5-match rule and manually change the result.  However, the program should change the "tie" wrestlers to the lesser place in order to accommodate the correct awarding of team points.  For example, a tie for 3rd place should result in both wrestlers awarded 4th place.