My recollection from several years back is that the Jefferson Scholarship and UVA admissions are entirely separate from one another. My kid was nominated by his high school GC for the Jefferson but opted not to proceed with applying to UVA. He did this early to avoid taking a classmates potential spot but I honestly forget how it was communicated.
The scholarship sought academic excellence consistent with UVAs standards but was primarily focused on leadership and service (similar to Duke/NC’s Robertson).
If your kid has been nominated for Jefferson there must have been a very strong letter of recommendation and narrative that will likely translate into the admissions application. If however you are asking if a 1300 will prevent a nomination that data I don’t believe exists publicly.
Wishing your kid well.