We use the Plagiarism plugin exclusively for assignments, and indeed experience this. Interesting to know that there is a way to deal with it in the Turnitin
Assignment 2 module. I had just assumed it was an intractable problem, and dealt with it in slightly more tedious ways.
Have you contacted Turnitin
support? Since they apparently account
for this scenario in their other products, I assume they would be familiar with accommodating it (or not) in the Plagiarism plugin.
I got curious myself, since this could save me and my teachers a lot of time, so I started looking through the Turnitin documentation. Unfortunately, this page about Similarity scoring scenarios
(Example 2) seems to suggest that the manual method that we use is the only option. That is, there is not a way with the Plagiarism plugin to make Turnitin ignore work directly through Moodle. You can always toggle and exclude sources when you are looking at the Similarity Report (which is what we do). However, that does not do anything to change the initial Similarity score that you see in Moodle, so you basically need to evaluate each one individually.
All that said, we try to be careful when we are assessing potential plagiarism. Of course, it is a pain if your workflow basically requires that students are always submitting two versions of the same thing. I guess we've just come to the conclusion that it is worth an extra minute or two of checking before starting a more serious conversation with a student about potential plagiarism.
I will be curious to hear if you learn about any different options for fixing this!