It doesn't matter which end comes first - .list entries work both ways - having it 'the wrong way' around changes nothing functionality wise, nor does the action of flipping it around to be the right way affect anything (an action that is easy and doesn't take long). It's both a trivial issue, and a trivial solve.
NY109 is a route where mileage increases to the west (rather than the east, per other W-E routes)*. Keep as is as it's not 'the wrong way'. Those who are going to notice are also going to notice that the chainage and our order match.
*Perhaps it was originally inventoried as a S-N route and then they decided that its more 'horizontal' than 'vertical', being a diagonal that does lean that way, when it came to directional signs.