There is one more reason to do resolution enhancement that I overlooked initially. That one also applies to B/W output.
Consider the chain of transformations applied to your original scans before they end up on the end-user's screen:
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Original scan -> [lossy transformation] -> E-book -> [lossy transformation] -> E-book rendered on end-user's screen.
The reason the first transformation is lossy is because things like rotations break the one-to-one relationship between source and destination pixels. The reason the second transformation is lossy is because the rendering scaling factor is generally non-integer, which also breaks one-to-one relationship between source and destination pixels.
To draw a parallel, consider the following scenario:
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Microphone -> [MP3 encoding] -> temporary MP3 file -> [MP3 encoding] -> final MP3 file -> MP3 player
It makes intuitive sense that increasing the bitrate of the first MP3 encoding results in a higher quality of the final MP3 file, even though the bitrate of the second encoding didn't change.
Scan Tailor experimental doesn't output 96 DPI images. It's just what your software shows when DPI information is missing. Usually what you get is input DPI times the resolution enhancement factor.