JFM The label switches between Output folder and Output prefix depending on whether you are exporting all animations or a single animation. Whether you export a single animation or all animations actually changes what you can specify in the box—whether it's the filename or just the folder name—so it makes sense for the label to change like this.
To be clear, when exporting a single animation as a PNG, if you name it something like walk.png, the exported PNG files will be named walk_00.png, walk_01.png, and so on.

When exporting all animations, each PNG image is automatically named using the animation name + frame number, so you cannot specify a prefix as shown above. Originally, if you selected Current in the Animations section and then switched to All, the section for specifying the suffix prefix is automatically removed, leaving only the folder name:

If you deliberately enter a name like walk.png here, it will be recognized as the folder name. A folder named walk.png will be created, and the images for each animation will be output into it.
I think Nate's point about the subfolder checkbox issue is that having only a 'Subfolder' checkbox leaves it ambiguous which criteria the user wants to be used to create subfolders. Therefore, it ultimately requires a variable to specify whether subfolders should be created based on skins, animations, or both. If this is specified, subfolders are created; if not, they are not. This seems the most reasonable approach. In other words, if the variable can be implemented, the checkbox should be unnecessary.
By the way, using the CLI for exports is not only more efficient, but also helps maintain consistent settings. You can save settings as JSON and reuse them, but loading them manually is tedious and often forgotten. Using the CLI helps prevent errors by loading the JSON within the command. We also provide a convenient shell script to make this process easier, which you may find useful: https://esotericsoftware.com/blog/New-export-shell-scripts