This is the fault/price of backwards compatibility. Most users of SQLite should just fire off a few pragmas on each connection:
PRAGMA journal_mode = WAL
PRAGMA foreign_keys = ON
# Something non-null
PRAGMA busy_timeout = 1000
# This is fine for most applications, but see the manual
PRAGMA synchronous = NORMAL
# If you use it as a file format
PRAGMA trusted_schema = OFF
You might need additional options, depending on the binding. E.g. Python applications should not use the defaults of the sqlite3 module, which are simply wrong (with no alternative except out-of-stdlib bindings pre-3.12): https://docs.python.org/3/library/sqlite3.html#transaction-c...
Also use strict tables. https://www.sqlite.org/stricttables.html