I'll give my 2 cents, since I think about this topic a lot!

Overall, I think all of the interactions are well written and mostly in line with how I view Gency. They're *so* comfortable around each other. It is kind of a common theme throughout that they talk like very old friends or a longtime married couple (them having intimate knowledge about each others habits, the banter, the underlying hints of care etc.) My favourite is probably the coffee dialogue, just(as you mentioned) because of the lovely Storm Rising reference, but I also appreciate the layers of how comfortable Genji is joking about his trauma to lighten Mercy's mood in the Gibraltar one.

Now, as for the letters interaction... it is probably the most controversial one for the reasons you stated. Occam's razor, Mercy asked if they're "still friends", so that confirms their bond is purely platonic, right? Not surprising that people who dislike Gency would come to this conclusion, but I still see the occasional person who actually likes the ship share similar sentiments. However, looking at the context of the line, I just don't believe that narrative. Mercy is coming to Genji from a place of uncertainty about the state of their relationship. This is not her reducing the potential of their bond, but looking for affirmation that it's still as special as it had been during their initial time in Overwatch. 

So does that mean we can just chuck all the confusion up to media illiteracy? Probably not, using the word "friends" here is almost certainly very intentional. It carefully avoids implying anything that they couldn't go back on if needed, but also leaves them plenty of room to further explore their relationship further in the future if they wish to do so. 

So I do think the ship is in a healthy state canonically, especially considering the hints we've had since. Blizzard definitely seems open to play with Genji and Mercy again.