I'm not sure about PRONOM in particular - it depends how they want to scope things - but I would argue that there are various cases where identification does not succeed but where it is useful to distinguish between them.
The primary use case is as a short-hand to distinguish the "failure to identify a format for a bitstream" case from the case where the actual identification process itself failed.
For example, when profiling the formats in the web archive, we hit so many malformed objects that identification often doesn't just fail - it crashes quite badly. So, when the identification process succeeds, but no format is identified, we record this as "application/octet-stream", reflecting the fact that all we know is that we have a bytestream. When the identification process itself fails, we return no format identifer at all, because we literally know nothing at all about the format. (We happen to shift everything over to MIME types rather than simply using PUIDs, but the issues are the same.)
Similarly, it can use useful to create identifiers for other edge cases:
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Folders
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Empty files
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Soft or hard links
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Various classes of block device
For web archives, only really the "empty file" case is worth considering. In the context of system analysis, as in personal digital archiving or forensics, these other cases become more important. This is probably why the 'fine free file' command is quite good at distinguishing between them.