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I don't think you understand the fundamental issue with this. It's a viewer, the expectation of a viewer is that it reads the file, not modifies the content. That's unexpected behavior that undermines the trust in software.
Besides, I have 5k book files in archive, plus 3-4k works in calibre combining multiple formats for files in archive. Over the years I checked maybe tens to hundreds random books when doing quality check or looking for issues on various devices. Some of them are not managed by calibre, and I don't even know what filles I touched, I need to write my own tool (and it can remove files while I'm at it).
The issue still stands. Unexpected behavior is not a desirable trait of any software.
Writing empty bookmark on first access makes no sense to anyone, considering 99% of the time you will never even use the feature.
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