It's hard to know when something is acceptable as behavior to society and when it is only acceptable as comedic entertainment when you are not part of that specific society.
There's also a difference between themes that are considered acceptable to share with minors and those that are considered adult only. Right now, the game is getting a ESRB-Teen (13+) rating in the US and PEGI-16 for UK and EU.
If Haurchefant had been portrayed closer to his JP characterization in the EN version when ARR was released the ESRB almost definitely would have rated the game M (17+), which would have blocked it from sale at most major US retailers. Even today, it might still get that M rating even though open discussion of same sex relationships has become more accepted since then. There are still a lot of conservatives that feel that children shouldn't be "corrupted" by exposure to such discussion.
Again, how did we not get the same story as the other languages got?
Oh, right. We did get the same story. Haurchefant might have been characterized differently in flavor text but his part in the story remains the same.
Again, in what way is the EN version different from the JP version that the story has been changed?
When it comes to Urianger, the EN version is actually closest to the original intent of the character. Urianger was supposed to be a mystic appearing at random times using cryptic and hard to understand language as sort of prophetic warnings. It worked for EN because of "Ye Olde English" (inaccurate as it is compared to the original) being a popular entertainment element but not all languages have an archaic version that's easily understood by modern audiences.
When the character became more popular than they expected, they slowly started dialing back on the eccentricities to make him more normal and brought him more directly into the story. That slow change has been part of his character development.