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The DB is not usually huge and shouldn't scale, so we thought it's fine to use an embedded DB. Since we're already using Postgresql it makes sense to use Postgres as the embedded DB, but I noticed Spring boot doesn't seem to support it like H2, after searching further online I've found a repo https://github.com/opentable/otj-pg-embedded that uses docket containers approach to "embedd" the db to our java code.
There is https://github.com/xerial/sqlite-jdbc, a full packaged sql lite for Java. We use it in production apps to store local user profile data. It works, is stable.