I know I can ignore it, but the question is why it does ask to overwrite... this shouldn't happen on proper archives. Also, as I've seen this in the past on different archives (not from you), that the multiple versions of the same file can have different file sizes (e.g. one with 120Kb and another with 1GB), so simply choosing "no to all" may end up with an extraction with incorrect files. Real question is, why your new archives do that.
Or avoid all of this, by choosing just the first file of each archive.