It's not just on vacuum. Rowids are reused whenever stuff is deleted from the end of the table:

    sqlite> CREATE TABLE t(x);
    sqlite> INSERT INTO t(x) VALUES ('foo'), ('bar');
    sqlite> SELECT rowid, x FROM t;
    1|foo
    2|bar
    sqlite> DELETE FROM t WHERE x='bar';
    sqlite> INSERT INTO t(x) VALUES ('baz');
    sqlite> SELECT rowid, x FROM t;
    1|foo
    2|baz

This is true even if rowid is aliased by an INTEGER PRIMARY KEY. Whenever a row is inserted, the new rowid is simply 1 greater than the largest rowid in use (or 1 for an empty table).

But Dflag is using:

   rowid INTEGER PRIMARY KEY AUTOINCREMENT

which prevents ids from being reused. So this isn't actually a problem for them, but the documentation could be clearer about it.