My tuppence worth. The addition of a breakable track is very laudible but does not really address the problem your design feature creates for users. All is well provided users stick with the provided software. That software manages the DTR signal. Most other software packages don't so users are stumped.
Given it is a feature that will be used by a few I would strongly recommend that you produce the board with the track cut but solderable for the few that will want to use the auto reset feature.
Then the board will work flawlessly with most serial software and build on the excellent reputation you have.