Dusty, I hope you're using classes for reused NPCs. For any tree-top NPCs you could probably have a single class to specify image clipping parameters (as well as tree color parameters) if that's not already the case. Definitely a solid move not to rely on filenames being updated for winter tiles and images.

Edit: Also, you could have repetition parameters. There's no reason to be sourcing more than just a single image for treetops or more than a single script for a single rectangular grid of treetop tiles.

Also, I don't get what the issue with the grass was. Only thing that I have a pet peeve with is when 4x4 square swamp grass tiles can't be cut. Some swamp grass tiles are diaganols though and so a 4x4 of those type probably shouldn't be cuttable. You could write up a debugging script that draws squares around cuttable grass and different smaller different-colored squares around would-be cuttable grass to help make that more consistent.

Some cliff tiling, in the meantime, is really annoying. It's like people forget proportions or something. I spent a ton of time normalizing cliff tiling in my time. Fortunately my work covered almost all of the overworld (at least the parts that haven't been retiled since). Of course proper cliff tiling can be restrictive with ledges. Air Asia was a really good example of bad cliff tiling where that wasn't the case.

I would consider it a tile error as well, since the problem is NPCs used as substitutes for tiles.