What should a teacher do with information about plagiarism before the final submission
I assume that somewhere you discuss plagiarism and the social good of respecting the IP of others. If not, plagiarism detection is just a "gotcha" that doesn't really benefit the students or your relationship with them. 

The following suggestion is offered tentatively, and might require tuning. It might also require research on the effect. 

If the tool is good enough to tell you in real time that something bad is occurring, it is also good enough to tell the student at that moment. So you could build that feature into the tool. 

However, there is, then, the danger that a student could game the system, modifying things just enough that the warning goes away. So it might be necessary for the warning given the student to also warn that not every "violation" will be reported to the student but will be reported to the instructor. 

Caveat: This was "seat of the pants - in the moment" design. I can't claim it is best practice. It is, however, based on the principle that fairness and communication are positive attributes in education. Help the student grow in many dimensions, not just the technical. 



In your discussions with students about plagiarism, be sure to include the concept of self plagiarism which many don't recognize as a problem since it doesn't violate IP rules. But does make derived research and attribution more difficult. 

And, like any lesson, it needs to be reinforced. Very little that you do just once will actually be learned. Active learninig is reinforcing as lecture is not. Class discussions about plagiarism and its tradeoffs (short term gain - long term  pain) might be useful.