Could be jobs could be the Ai doing dumb shit, yea could be that bug you speak about, tho I am unsure how going from the center of a races sector to a sector literally next to that it with a line of sight of 1 gate between them makes the Ai decide to jump to around to the outer edges of the races sectors and back too get too the destination which is what is going on a lot for me when I order pilots of ships I am just a passenger on to take me to some station a sector over I wind up seeing the order path looping up 2-5 sectors before reaching the destination which as Is said with my own eye-balls I can see is only 1 gate away from current destination.
I do not think it is this galaxy's fault I believe it is the Ai Logic in general which a chore to be had at the best of times.
I am also not very familiar with a lot of complex tasks yet, I barely started my own station some 80 hours into this play I was lacking hardware to run the game above a consistent 40 on launch and last few months have been only time I had to toy with it in a playable state and have been swapping mods like crazy but coming to an idea of what I like atm in this mod list.
Mods I run.
I lean towards the savvy side a bit and If I can wrap my head around this XML crap (which I hate I like LUA and Python)
I have been wanting to make a diverse larger universe myself using the galaxy editor you can grab here I am sure you have advice on it hope its pretty simple and not all manual XML edits because I probably won't bother if it is.
But I like this design you have going, I was going to fire up a map of X3 then maybe Rebirth and merge those into a seamless addon for this.
With some law behind them, like you cant just simply find the gate for X3 its more of a task like you eventually find the gate but it's destroyed initially as you'd expect and you will have to rebuild it however once built you get access too X3's sectors along with the Split Race which I know is not released yet but a nice way to lore in why there is no real Split presence in X4 as all but the traders and civs got stuck behind a broken gate during the old wars when the gates were broken.
Same deal with Rebirth, I was just waiting for the DLC but I could setup the universe now and do testing before then only it just adds more sectors and a more spread out kind of universe to what exists now.
I have no idea if the whole sector take over thing is in the game yet but I know it is supposed to be a thing in X4 eventually but that is what I had in mind for most of my expanded galaxy to work as
you would have a few obvious sector choices for existing races to start with to get the economy moving in those unreachable by player sectors but the vast majority will be different from a time period closer to X4 post X3 wars and majority of them un-claimed by any race leaving the olde now redesigned galaxys open for the taking or loosing it would be quite interesting to see how it shapes up after races begin to take claim and fight to expand naturally across the galaxy.