But now every user of SQLite needs to deal with a library that's larger, and includes non-critical functionality that goes unused.
The whole point of using SQLite in the first place is to avoid such overhead, knowing full well that some non-essential functionality is being lost as part of this tradeoff.
I think it's far more important to keep SQLite small and nimble for the many users who are facing constraints beyond their control (imposed by limited hardware resources, for instance), rather than bloating it for the sake of a small number of users who are unwilling (or too lazy?) to write proper manual migration scripts now and then.