Well we know in space the Valks and beyond should close the intake covers on the engines. I believe except for animation mistakes they do. I assume this is to protect the blade turbines from dust and micrometeors in space. The Fp's cover the intakes because they arent being used in space, and it gives the plane a new point of armor to protect a vulnerable area. i have always assumed that most VF series fighters cannot fly in atmosphgere with their packs on, the 19 and 21 being rare exceptions.
As to what the packs contain; alot of them have nozzles for extra maneuvering in space, so I assume they have propellant for those, provide armor, and past the 11 series have micro missile pods for extra offensive capabilities.