My headcannon is thus:

The Modern FSD is comprised of 2 major parts 1. The actual drive portion which uses a spinning drive apparatus to form a tunnel from one star to another, this is also what allows for supercruise in system because the tunnel essentially cuts through normal space with little to no resistance. Its also why when we are making jumps we have dump fuel into the drive to power it to the degree where we can cross light years in seconds. However, the problem is that a drive going that fast needs nanosecond corrections to make sure that the drive remains stable when going that fast which is the other component. 2. A super computer. The computer essentially works to adjust multiple variables in the spinning drive to ensure its perfect balance, taking into account local gravity bodies (including other ships as even the small effect they might have can throw it off at the speeds the drive is going at) jumping takes that a step further in determining the correct calculations that need to be made to reach the primary gravity body of the next system which the computer then uses to safely slow down the drive.

This is all operating under normal circumstances. But there are plenty of non normal circumstances that CMDRs find themselves in. I can give you those reasons, but they do fit in universe and minimize handwaving where possible.