It absolutely does matter that the area of effect is covering your gravity well. In most cases, for asteroids, one PJI will cover the whole well. For the larger planets it take at least 2 if not 3 to cover the entire area. There are also some starbase upgrades on one race (i think) that can provide the same service. I have noticed for all abilities (capital and building alike) that the actual distance covered is a frigates length past the circle showing. So you could have ships still slowed by the PJI even though the purple circle isn't covering them.

I believe you are reffering to the jump degradation abilities that SB's get. this does not lengthen the charge up time of a jump, but instead deals damage (i believe 30%) and drains ALL of the ships antimatter once it completes its jump.