As I understand jump 8and I may well be wrong), the vector must be calculated to be in the correct vector at the correct time, and, as you say, IISS takes all care to avoid missjumps, making them anecdotical to unheard of.
There's a jump space "vector" - the 2D plot used for jump shadows and masking that Mr. Miller told Wil to use for his calculations - and a real space vector. There's a real space vector which is carried through jump. A "helpful" real space vector carried through jump cannot be calculated with the precision you assume because of the temporal accuracy of jump drive.
As you don't know the exact time of incoming X-boat arrival (it may be at anytime along a time span (version dependent), you cannot have the X-boat in the jumping vector when it arrives, though its correct vector is constantly updated in wait of the arrival.
The temporal accuracy of jump means you cannot be that precise and the nature of X-boat operations means you don't need to be that precise. Waiting a few more minutes or a few more hours to jump because you want to tweak a vector isn't going to help because jump's temporal accuracy introduces a far greater error than the correction you hope to make.
Here's the bit you've overlooked: X-boats aren't "aiming" for the 100D limit. They don't care about traveling to planets, belts, or whatnot. They don't need to worry about creating a vector which will help them in-system. They don't want to travel in-system at all.
Instead, X-boats are 'aiming" for that 12K km radius sphere out in the system somewhere and they want a vector which will leave them moving at either rest or at a low velocity within that sphere.
Let's look at a jump between Ruie and Regina for both a free trader and an X-boat. (Yes, there is not a X-boat link between the two. Let's just pretend there is one for this example.)
I'm in my Beowulf, I'm going to Ruie, and I'm calculating what real space vector I want to carry through jump space. From Regina's frame of reference, Ruie the system is moving along a vector but Ruie the planet is moving too and moving along constantly changing vectors.
Because I'm going to Ruie the planet, I'm going to take into account Ruie the planet's range of vectors within the range of times I'm likely to arrive. Using that data, I'm going to select the a "best case" real space vector which will help me travel to Ruie the planet after exiting jump. That "best case" vector is going to be one that works for most of my potential arrival times. That "best case" vector is one that will have me already moving towards Ruie when I arrive.
Now I'm in an X-boat and I'm jumping between Regina and Ruie again. I'm not interesting in traveling to Ruie the planet this time, so it's vectors don't matter. I'm not interested in traveling to anywhere in the Ruie system, I just want to pop out at the X-boat station. That means I'm only interested in the vector of the Ruie system as seen from Regina.
In this case, I'm going to choose a real space vector that has the best chance of leaving me at "rest" with respect to Ruie the system. Again, not knowing precisely when I'll arrive means my choice won't be perfect and my X-boat will emerge with a vector that doesn't quite leave me at rest. I can get pretty close, however, closer than I can with Ruie the planet.
Of course, this does not preclude the jumping of the outgoing X-boat in about an hour as you say, jsut may make the incoming one to wait for a little more (but it is not significant).
I'm not saying the out-going boat departs within an hour of the in-coming boat's arrival. I'm saying the tender/station can rendezvous with the in-coming boat within an hour because at one gee it can traverse the 12K km radius sphere within an hour.
The out-going X-boat is going to depart with it is "loaded". It's been already been staged with fuel and a pilot aboard. It's already been given an "at rest" vector for the next system. All it's waiting for are those messages. Once they're aboard, the 'boat can jump. It could wait 15 minutes. It could wait one hour. It could wait longer, especially if there are passengers and parcels to transfer. All that matters is whether the X-boat is loaded or not. When the load is aboard, that 'boat is gone.