See a university may offer many courses hence the university ranking is different while engineering rankings are exclusively for technical courses offered by the institutes or universities. If you notice, a large number in the engineering rankings belong to technical institutes more popular or known for technical courses. There may be cases where a university will be in both and the ranking may be different. Thats because the ranking in engineering is just for the technical courses while the university ranking would be for all the other courses. This is the simplest I can explain. The parameters used by NIRF are given below

Teaching Learning & Resources

Research and Professional Practice

Graduation Outcome

Outreach & Inclusivity

Perception of the institute

The rankings are an overall picture to give you an idea of which university may be good. So you could in essence take it like that.