One reason for that: appdata is the microsoft mandated official place to store configuration and saves for programs. The name speaks for itself, really. Other operating systems have similar schemes which mandate specific locations for specific data. Two reasons among many being easier manageabke backup and the ability to use specific storage options or special handling by the operating system for specific data.
When every program stores stuff whereever it pleases BAD things happen. Microsoft or specifically the users of old windows versions learned that the hard way. I don't think "Documents" should be filled with program data, it is where the user tries to store his documents and most people will have a hard time even managing their own stuff in there.
So the sad news is: Players who want to mod need the knowledge where and how to access the location where to put their mods and there exists old and wrong information on the net. Yeah, can lead to confusion, can't be avoided really.
My guess is that the Mods folder inside the game folder will always work for Mods, but there are other problems that could turn up. Like any of the operating systems used for 7days could police those folders and for example disable the whole program start. That is fine if you know what you are doing, you'll manage. But seriously, if some noob asks you where to put a mod you give out the new location or you are responsible for all the confusion and trouble following.
It is like repairing your computer or worse a power supply. If you know what you are doing, go ahead. But please leave that sticker on that promises death and small pox if anyone even just opens that case