It's an extra +4 on the control roll. The control roll is already a +2, so with a average piloting of 4 or 5, you are looking at needing a 10 or 11 to do it. If this roll fails, you have to spend additional blocks of time until you succeed, with each block of time being equal to 2d6-Margin of Success. Failure means it could take upwards of 10 extra hours (worst case) for a failed roll (More if you were moving). Which if you eventually make it in a reasonable amount of time, would still be a net gain for your dropships, but eventually lack of success would just be delaying them from reaching the planet. (numbers from section on making the jump in SO pg 88)
Once you do make the jump you make another control roll. You get your margin of success as a bonus, but the target number gets increased for every point of damage your K-F drive has taken. Success is success, but failure applies 1d6*2*Margin of Failure capital scale damage to each armor facing of the JumpShip and every dropship it carries. In addition the K-F drive integrity is reduced by the margin of failure, and if that reaches 0, the JumpShip and all of it's dropships are destroyed by the jump process. (SO pg 89) (I find it interesting that a MoF of 2 on this roll could potentially do enough damage to destroy any JumpShip in TRO 3057r from the damage alone, on any jump)
Nothing in the rules apparently makes jumping to a non-standard point more dangerous, since the two control rolls are not connected at all. Apparently jumping to those points just potentially takes a lot longer, and if they don't succeed at the jump calculations quickly, it could potentially waste a lot of everyone's time. Time is money, especially in transportation. If I had to guess, the nonstandard points aren't used because or the random chance of huge amounts of time being wasted.
Another thing to consider is can the Jump Sail actually charge the drive as effectively from the nonstandard point? If it is an L1 point between a planet and it's moon, how much time will be spent in the planet's shadow relative to the sun, extending the charging process? This potentially wastes even more of the JumpShip's time, possibly a much more significant amount of time.
Something else to consider is how close to the ground do you want your JumpShip. The closer to a planet it gets, the easier it is for someone to try something stupid. With much less turnaround from the surface to an L1 point between a planet and it's moon than to the zenith/nadir points of the star, it could be riskier to jump to those spots. The JumpShip can't exactly run either, since it's max burn is 1/10th the max burn of the slowest thing that might try something, and leaving the very small L1 point would mean you can't jump until you get somewhere else (at 1/10th the burn speed of the slowest dropship). If your sail is deployed you have to choose whether you are gonna get boarded or lose the sail 'cause they break when you move around with them deployed. (Fluff in SO on pg 124 and Advanced Battleforce Rules in SO pg 276)