I think clearly the character for village does actually factor in to the intended solution for the epitaph. Even in my own solution, the name for Qilian station (in Kanji?) is 唭哩岸, which does actually contain 里, but I didn’t notice that until way more recently because of the extra box shape attached to it (and also because my stellar understanding of Japanese made me think they were different for a while even after I noticed the visual similarity 
)
I honestly don’t know why Kinzo would become so upset over this. Sure; it contains the same character, but I don’t know what part of that is so misleading that Kinzo wouldn’t be happy with it. Would he have gone and removed all associated characters from everywhere else around the mansion? It seems like a stretch. Perhaps the implication that Maria was involved with the key was a bit much for him, but I’m genuinely rather confused. Is it because it distracted from the purpose of the epitaph? Is it because Kinzo did not want additional factors to change the difficulty of his epitaph? Is it because he was upset that he thought Rosa was the one coming to an answer? I don’t know, I guess I can only hope we’ll find out.
I think the reason Ryukishi draws attention to it when he does (and Kinzo’s anger over it) probably has something to do with poking readers towards the solution, but I’m sure the connection is intended to be a bit more deep than that. Maybe that connection would be a bit more apparent to someone who understands Japanese, but I don’t even know how 哩 is different to 里 in terms of its use or meaning.
As for the unknown book I’m now certain Eva actually does state (in our E3P10 video) ‘I need to check an atlas’ but somehow we both completely glazed over that fact. Perhaps having read that was what compelled me to not give up on the journey through Wikipedia pages on Taiwan at the time, but it definitely didn’t factor in to the solution consciously. I think part of how those clues are intended to work was worked out by @mimsy during ep5 here, but because of my methodology they weren’t necessary.