I agree that is unclear for an introduction, and that the article could have been written better. The “pile-of-files” they are referencing isn’t a filesystem of arbitrary and unstructured binary data stored for humans to look at later (like your Helpdesk attachments), but rather structured and specific data for an application to read in a well-defined manner.
Your Helpdesk example used SQLServer problematically because a SQL database shouldn’t be used as an arbitrary file store. But if you know what the file structure is and have a reasonable grasp for how it might scale (that each binary blob is small, that each user only adds one row to the database, etc), there are huge advantages to “a SQLite table with lots of binary and text columns” versus “a folder with lots of binary and text files.” And if those text files are just small key-value pairs then maybe they should also go in SQLite.
Did you read the article? This isn’t about storing blobs as data in SQLite, but rather using SQLite-formatted databases as the file format for an application.
As a simple example, Word documents are just zipped XML text files (try unzipping a .docx and looking inside). Instead of using this, you could a SQLite .db file (probably with a different extension), translating the XML files into tables, and folders into databases. The OpenOffice case study has more details: https://sqlite.org/affcase1.html
Your Helpdesk example used SQLServer problematically because a SQL database shouldn’t be used as an arbitrary file store. But if you know what the file structure is and have a reasonable grasp for how it might scale (that each binary blob is small, that each user only adds one row to the database, etc), there are huge advantages to “a SQLite table with lots of binary and text columns” versus “a folder with lots of binary and text files.” And if those text files are just small key-value pairs then maybe they should also go in SQLite.