The proposal to use sqlite database files instead of zip files falls under the precondition that an attacker can submit a maliciously crafted database file. So

The proposal to use sqlite database files instead of zip files falls under the precondition that an attacker can submit a maliciously crafted database file. So the security concerns apply. SQLitte is mostly used in situations where neither the database nor the SQL statements can be provided by the attacker. If SQLite is used to exchange data both of these attack vectors are available.