Manual dependency injection is fine, but it doesn't scale. Especially when you start refactoring things and dependencies need to be moved around.

The other issue is dynamic configuration. How do you handle replacing certain dependencies, e.g. for testing, or different runtime profiles? You could try to implement your own solution, but the more features you add, the closer you'd get to a custom DI framework. And then you'd have an actual mess, a naive non-standard solution for a solved problem, because you didn't want to read the manual for the standard implementation.

By the way, Spring dependency injection is mainly based on types. Annotations are not strictly necessary, you can interact with the Spring context in a procedural/functional manner, if you think that makes it better. You can also configure MVC (synchronous Servlet-based web) or Webflux (async web) routes functionally.

When a bean is missing, the app will fail to start, and you will get an error message explaning what's missing and which class depends on it. The easiest way to ensure this doesn't happen is to keep the empty @SpringBootTest test case that comes with the template. It doesn't have any assertions, but it will spin up a full Spring context, and fail if there is a configuration problem.

The only complicated part about Spring Boot is how the framework itself can be reconfigured through dependency injection. When you provide a certain "bean", this can affect the auto-configuration, so that other beans, which you might expect, are no longer automatically created. To debug this behavior, check out the relevant AutoConfiguration class (in your IDE, use the "go to class" shortcut and type something like FooAutoConfi..., e.g. JdbcAutoConfiguration).

In a good codebase, the configuration itself would be tested. For instance, if you did something a bit more complicated like connecting two JDBC databases at the same time, you would test that it read the configuration from the right sources and provides the expected beans.