I think the problem with Naviance is not coming from the HS input. All information provided by the high school are there (GPA = 3.85 and latest SAT=1440).
The issue is exactly what you said - although I picked aerospace engineering as a major, the results are not accurate - a lot of competitive schools for this major came up as safety (Purdue, Univ. of Michigan, Univ of Virginia) while with these are clearly a reach with these stats based on information I have from students that applied this year.
What means posters on CC ?