Think of Lightroom or automation over files. Many semi professionals from wedding photographers to designers want some form of batch automation and organization system over their files.

Several megabytes/gigabytes assets and you want to extract metadata, a preview, running as a batch some filter/compression/, conversion to CMYK, text injection ... fast partial read/write access would be nice. Right now, most reads are performed through indexes because those files are slow to read.

If we take 10k sqlite files and want to retrieve a row, we would be around 3s on SSD, maintaining preemptive indexes become less important for a lot of use cases.

Change management and versioning also becomes quite efficient - sqlite can be configured to not offset bytes, so CVS like Epic Lore can efficiently delta the files and store minimal delta, or the file format itself can keep its edit history. Oh and it's 3x-10x less bytes without compressing the whole thing, so pages are stable through time.

About needing SQLite client, it's real but it's roughly the same size as an XML parser.