hmmm you know Rey, out of all the logical comments everyone (including you) gave. There is just one Most logical factor that everyone forgot. Planets move, asteroids move, galaxy's move, universe's move. And they all move in circles.
If ship "A" were to jump from point "Y" to point "X" then there is a logical factor that must take place. Which is the time it takes to travel.
Logical conclusions of the theory of jump gates are that the ship going through a jump gate would travel at the speed of light which in theory is still too slow given the fact the the universe is a really massive (if not HUGE) place. At the current state, the speed of light is the fastest way of travel known to man which is also yet to be proven by man as we dont have that kind of technology. Everything is still theoretical and I dont think we will ever have the means to create that technology to prove the theory correct.
Anyways back on topic. What I am trying to say is that it doesnt matter where the gates should be placed in a system, what REALLY should matter is where the gates are pointing and an accurate calculation of data must be present.
Example: If I was to shoot myself with a rocket from the moon to mars, I would be thrown in a vector course towards mars with nothing but momentum. In that case I would have to point where mars would be in the time it would take me to get there which would be say....a course of 8 months (roughly calculated) and then also point where mars would be in 8 months which is where I would have to point my rocket before luanch in order to be EXACTLY on target.
Likewise the jumpgates have a similar function and since they calculate in the speed of light, the numbers would be too much for us to even comprehend. As long as your pointed the right way, it doesn't matter where you are as long as its the right way and also (one more thing everyone forgets) as long as you are not facing towards a solid object otherwise you will die.
Thus I conclude this debate kinda pointless and also shows the reason as too why everything seems out of place in OP's maps
Right time for me to go to work.