Not sure why the sibling posters determined s/flatfile/flatfiles/ the most interesting part of your question.
There are advantages over SQLite, eg: the ability to use unix command line tools against the file directly.
In my view SQLite has more advantages though.
Of course principled command-line tools for text (e.g. awk) and the possibility of running arbitrary SQL queries on a database blur the line, but the distinction between files that are read or written once as a step in a transformation pipeline or as something to load or save and databases that represent a persistent state, with transactions, remains sharp.
Looking back, you seem to be right. I thought mlthoughts2018 was referring to a specific file format, or at least a specific library because (1) They made up that weird terminology "flatfile" which looks like product name instead of just saying "plain text file" ... I wonder why they did that? (2) They made claims about transactional integrity with a WAL-like log. Now I realise they were suggesting you homebrew that anew for each fresh project that needs to store data! The idea that this would be easier than just using SQLite's existing mechanisms is so bizarre it didn't even enter my head they could've meant that.
Why would I use flatfile (aside from the fact I've never heard of it) over SQLite? So far you've just said SQLite has some features you can't imagine I'd ever need, but even if that were true then it wouldn't be a problem in itself. What are things that are actually bad about SQLite compared to the alternative you're suggesting?