The "3" refers to the file format (or rather, represents a breaking file format change vs 2), which the devs have committed to keep backward-compatible until 2050. https://sqlite.org/lts.html
Oooh I'd forgotten about that! I'm keen on the real (non-rowid) primary keys and covering indexes. I'm not sure about defaulting to decimal math, but I suppose the reasoning makes sense
They even had an sqlite4:
https://sqlite.org/src4/doc/trunk/www/design.wiki