There are some programs (HEOP/EOP/SEEK/College Discovery), for students who are academically/financially disadvantage, but student must indicate that they are applying to this program on the application. other than the use of a fee waiver I have never heard of the low income plus factor.
Are students evaluated in context of what their school offers? yes. This is where the profile comes into place. Your school profile with give the demographics of your school; graduation rate; percentage of students attending 2/4 year college. 5 of title I students, % of students with disabilities etc. If youare from a school which is 80% title I there is a good chance that the AO reading your application is going to be able to figure out that the odds are that you are a low income student.