If you need to do a lot of inserts (or updates, etc), the slowest possible way to do them is to do them outside of a transaction. The fastest way to do them is to wrap them all into a single transaction.
This doesn't seem to contradict the comment you're replying to. They're suggesting wrapping operations into transactions in batches e.g. (just making some numbers up) if you have 100,000 inserts maybe you'd do 100 transactions of 1000 inserts each. I wouldn't call that "the opposite" of your one mega-transaction suggestion. In fact I'd expect it to still have most or all of the speed benefit of using one single transaction, or potentially even be slightly faster.
For serialized writers in any system I'm sure keeping a transaction open as long as possible is the ideal case for throughput, but there's other problems with that in a CRUD app no?
But to answer your question at face value, one common use for SQLite is as a file format for complex desktop apps, or perhaps a game save format for certain types of games (mostly the non-realtime types). One great advantage to this is that if you use a DB migration library, you ensure backwards compatibility with previous versions of your saved files. However, it's easy to imagine a fair bit of data getting inserted into such a new file each time it is created. It might only be 5000 rows, but I'd prefer to not have to wait 5 seconds just to persist it, if a single change can make it 0.05 seconds.