Spotlight comments replaced during "Keep Both" copy

I have noted this behavior in El Capitan 10.11.6 on a MacBook Pro "Summer 2012" model:

Let's say you have two files of the same name, one in Folder A, and one in Folder B.

Furthermore, let's say the two files have different Spotlight comments.

If you copy the file in Folder A to Folder B, and choose "Keep Both", the file originally in Folder B will have its Spotlight comments replaced with the Spotlight comments from the file originally in Folder A. Not good!

This is important to be, because I store MD5 hashes of the file in the Spotlight comments so I can use them to find exact file duplicates.

Anyone else see this behavior? How far back does this date??