I'll note that the metadata is handled correctly by the CLI's .backup command or you can "VACUUM INTO <somewhere>"¹, so if you're just attempting to use .dump for the sake of backup there are probably better options available anyway.
But yeah, I was surprised when I chased down a bug that was caused by a missing application_id following a restore from .dump output. I did a search at the time and noticed it had been reported to the sqlite folks on their forums a few times, so presumably I'm missing the reasoning behind not including it.
sqlite> select * from pragma_application_id();
0
sqlite> select * from pragma_user_version();
0It is just another thing to be aware of if you're trying to store your database in your git repository with a filter, and want it to roundtrip correctly.