I don't understand your SQLite concern, is it purely that it doesn't ship with a tool to import fixed width data? I often wrap (or have to wrap) such loads from various sources in a perl script, so that I can apply some logic and error handling when inserting millions of rows into SQLite. This isn't a lot of work and it allows for greater control. Depending on what your code is like SQLite would likely perform better than MariaDB on lower end SBCs. For context I use SQLite with a Mojolicious front end, I recreate the data on a nightly basis, millions of rows, it performs very well.

Regarding how to replicate your system from emmc to sd card, you could use dd to create an image you'd then write the target sd cards.