Turnitin is not a useful tool for students.
The appropriate use of Turnitin is to provide a similarity report to someone familiar with academic writing and the relevant field, which that person can use to screen for suspicious clues that could lead them to suspect plagiarism. It cannot help an honest student author, because if that author understands the customs surrounding plagiarism, they should already know that they have not plagiarised; whereas if they don't understand the customs, the Turnitin report is useless to them anyway.
The OP doesn't need to do anything about this.
So there is no reason for the OP to try and fiddle with the Turnitin settings, because they shouldn't use Turnitin again (atleast until they get an academic job themselves). If their PhD thesis is going to be run through Turnitin, the person will presumably either immediately see that the flagged document is the OPs dissertation, or be able to confirm quickly that the OP indeed wrote their own dissertation. It is then their problem to get Turnitin to tell them about other similarities (but I think Turnitin does multiple sources anyway).
But it may look suspicious
There is a small caveat to my first claim: A plagiarizing student could use Turnitin to try and hide the evidence of their transgression. Uploading a copy of the dissertation could have been an attempt to mask whatever hits Turnitin still finds. So I wouldn't be surprised if OP's dissertation receives more scrutiny regarding plagiarism than usual - but not because of a 100% Turnitin score, but because OPs behaviour seems suspicious.