Yes, that is because the GM2 auto tile feature requires 16 tiles to work (with one being transparent) so if you look closely you can see that there are two diagonal tiles that aren't in the normal tiles.
Ah that's not what I mean!
In the autotiles folder you have, for spring:
spring_dirtpath_auto.png
spring_grass_dirt_auto.png
spring_grass_soil_auto.png
spring_grass_transparent_auto.png
spring_soil_auto.png
spring_water_auto.png
so six different spring tilesets.
In `all tiles.png` you have what looks like from the top down
spring grass transparent
spring grass dirt
spring grass soil
spring water
But between what you just said and from staring at all of these files now, I'm guessing that the extra tiles that exist in `all tiles.png` are doing the same job as the extra files in the autotiles folder?
If you can't tell I've never used GM2 (I'm using Godot) and am new to this so thank you for your patience :D
Ah now I get what you mean. Okay so you have spring_soil_auto and spring_dirthpath_auto in the autotile folder because they are "flipped" versions from spring_grass_dirt and spring_grass_soil.
So when you have a big green area you can have a second layer and draw in soil and dirt directly, as in pathing it rather than map out everything in one go. I'm also not a dev, but I found that easier when setting up test levels to try my auto tiles.
Hope that makes sense!