You forgot my favorite - when someone complains here in the forums and they ask that you give specifics as if we haven't complained about the same things so many times that most of us old Alpha/Beta backers have just given up reporting anymore. your post is one they should take seriously, but I no longer have any hope for that.
It's an entirely justified response to the kind of one liner drive-by posts you sometimes see in patch note discussions. Imagine a post like: "CQC? Srsly FDev? Fix g congruency first!111" Tell that a dev or game designer who might not have followed the the whole forum the whole time. He will know exactly nothing about what you'd like to have changed. Even if they had, they might still not know what congruency is for that specific person. Typical software engineering problem not specific to games...
On the other hand, this OP is specific enough, so we know which incongruences they're talking about. And I have to agree - Elite has tons of such incongruences. Problem is: While some of the mentioned ones are definitely fixable (if fixing them is prioritized enough), they will never be all fixed. Hazarding wild guesses what prevents the devs/designers from fixing them - especially implying they might have no clue that the issues are there or that they are just too incompetent to fix them, will also not get the fixable issues fixed any faster. You have to accept that their time and budget is limited.
However: Understanding why not all of those issues are fixable in the first place and having realistic expectations does help both sides - a lot. Heh, so much for managing my expectations.
The way I see it, the congruency issue during moment-to-moment game world simulation is a persistence and logic issue.
Elite is an instanced game and as such an instanced game it will only simulate a small slice of the game world around you. Leave your current instance and come back later - the game will only know and react to your previous actions if the devs have explicitly programmed it to remember them and to react accordingly. It's the same as in GTA games. Wreak havoc at a crossing, lose the cops by driving around a couple of blocks and come back to that crossing - nobody will remember that you just crashed a jet fighter into a school bus, beat up the fire fighters and pulled a guy out of his car to escape the arriving police. That's because the game doesn't store all that. It just loaded the particular static part of the town again and populated it according to some randomization and maybe some paramters that persisted. Add several layers of instancing (normal flight, supercruise, witchspace) and it all gets pretty complicated to the point that fixing general congruency issues takes a lot more time and thought than anyone might think from the outside. Worse: Because you coul get into limitless details with the congruency, you will never be able to store all your actions and provide the game world with a unfailingly reasonable (from a social human being perspective) response. The complexity is simply not manageable within a time and budget limit.
There is a theoretical alternative: If you had one instance of the game's world and every object/character within, much of that issue would be solvable "pretty easily". You could see the ships approaching a RES in supercruise and later find it there. You could buy X amount of ware Y from a station and every other player would see the lowered supply. Imaging that across the game's galaxy though and you'll find that you'd also have to have a central server(-cluster) with practically limitless storage and CPU resources, not to mention network bandwidth. Apart from maybe having the technical capabilities, you'd also have somebody programming all the logic, which may take surprisingly long.
So, abstraction and incongruences aren't going anywhere any time soon. Especially not with some patches half a year after release. Pointing them out in a more constructive manner (the thread title is about the opposite of constructive) might help in small steps, eventually.
There are of course things that might and should be improved, partly by avoiding the issue by means of game design: E.g. implement an extensive mission system (whichever form that may take, apart from amounts of resources that I doubt FDev have available), that provides occupation and financing for players in their various careers. In return: limit the spawning of pirates and wanted ships in RES/Nav Points to instanced missions and rare occasions rather than having a constant stream of them. There can't be that many stupid pirates in the galaxy waiting to be shot up after all.

Oh, and have stations attack the OP if he has sided with their enemy factions recently (edit: Provided they are
scanned). That should really be a relatively simple fix.