As good as Logan was, do you think that in some way taints the other X-Men movies now that we know it’s all heading for an unhappy ending where mutants have been scienced out of the gene pool and the X-Men are all dead?

Not really. It’s one possible ending among many, and X-Men have been doing the “averting the dystopic future” thing since 1981. So I don’t have a problem with the fact that Logan is a particularly bleak dystopian future. 

What I have more of a problem with, as I’ve stated before, is that the X-creators have something of a failure in imaging anything but dystopian futures.