First and foremost, that I don't get to decide where things go on my own machine, and that if I do regardless, because developers didn't follow a simple standar

First and foremost, that I don't get to decide where things go on my own machine, and that if I do regardless, because developers didn't follow a simple standard and instead decided to hardcode things that shouldn't be hardcoded - which is just about the first thing every dev is taught not to do - things will break. You may not find it important but is it an issue or not?