Again, main issue here is Licensing. Sometimes it's just impossible to get all the rights necessary to have this accomplished. And if you can't get the rights you are liable to be sued. Do remember that these official companies are profiting of these releases and as such the original companies that put in work are able to sue if proper steps are not taken.
Fans on the other hand don't have this handicap and can literally, LITERALLY, do whatever the fuck they want. I could, theoretically, add in Linkin Park music as the OST or add in functionality to the game that wasn't there before. And not only do I need not get the rights to either the company who made the game, I don't even need to bother with music licensing.
And in regards to ALL of this, if you are going to sit there and go "well I'm not going to spend money because there is a free, better, version out there" then do just that. I personally have bought many visual novels and never opened them purely because I played the fan translated releases when they came out but I do in fact want to support the developers. Just like games I used to pirate long ago I all have in either a digital or physical paid copy. If content is so important to you, get the fan translated edition, play the fan translated edition. But if you want to support the sales of a game you enjoy, go purchase it, regardless of which version you play.
Add to this is a person didn't even know of everything you are talking about they would still purchase the game, play it, and that's that. It's not like the company is going "Hey everyone buying this product, look there is a fan version out there that has a shitload more content then the one we put out...just saying."
If the customer doesn't know, the customer won't care. So you might give a crap because you know, but many others who actually buy the game might not know this and therefore don't care.