Save Each Artboard to a Separate File waits until end to save all files at once.
When using the option to save each artboard to a separate file, illustrator keeps all the saved files as TMP files and doesn't finalize them until all artboards have already been exported to the TMP file. This isn't an issue for small files with a few artboards but causes delays with larger files / number of artboards because the AI files are all saved out at once at the very end of the process.
It would be more efficient for some workflows if the AI files were finalized along the way so that they can be further processed by others while the rest of the artboards are being saved.
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I suspect it’d be just slower, but it makes sense. 'Progressive JPEG' style, the result is always available.