For each file it needs to write, will it look into each folder it's writing to and then name+increment each file based on the content within the folder rather than based on a global name for all files being created? 
yes, that is correct, the file renaming is on a per file basis.
In actual fact, we don't recommend using the resize option in the Upload anymore since we released image resizer.
It's better to only upload the original sized file, then use Image resizer to create the resized images on a page by page basis.
this way you can decide at a later date that the size you are using is to small, then just change the image settings to have it resized on that page, rather than have to re upload the image.
image resizer is much more flexible.
