You just call sqlite3 as you wrote. At this time there is just an empty file. Then you set your pragmas. The database with all its settings will be written after creating the first table. And the time of writing with all the environment variables is important. Just then the database is really created. So just set your pragmas before creating the first table.
e.g.
sqlite3 test.db
opens sqlite, nothing is written at that time
pragma encoding=utf16;
there is still nothing written
.quit
closes sqlite, an empty file test.db gets created
sqlite3 test.db
opens sqlite
pragma encoding = utf16;
pragma nnnn=xxx;
sets the pragma(s), the file test.db is still empty
create table test (testid integer);
now the database gets really created and the database file test.db gets written with content