How about varying implementations of a service interface. Let's say I have a Scheduler interface and I want to have multiple implementations; maybe one is CronScheduler, another is RandomScheduler, another is BlueMoonScheduler. Each of these schedulers have their own properties and configuration values. I might want to choose, per environment or deployment context, which service implementation to use.
Annotation configuration makes this (near?) impossible to dynamically wire and configure these scenarios and make them tailored to the environment or deployment scenario. Annotations are generally "static" and do not follow a configuration-as-code approach to application deployment.
An external configuration file, as offered by Spring's original (less "favored") XML style, allowed a more composable and sophisticated configuration-as-code approach. Maybe that's a negative, putting that much power into the hands of the service administrator. But as I stated originally, in my experience, having statically defined annotation driven configuration and/or dependency injection has caused more problems than it has solved.
all of your scenarios are trivial to implement with annotations
Off the top of my head, you could drop a `@Profile` or `@ConditionalOnProperty` annotation on each of your different schedulers and pick them at launch time simply by adding the profile you want to the arguments or the environment. That assumes you want to choose one for the whole app. If you want to have different ones in different locations, you can dynamically load beans in code. Or if you want them loaded entirely with annotations, you could define differently named beans for each context, and include `@Qualifier`s on them and in the locations they're being used.
Which isn't to say that annotations are perfect, but dynamic runtime configuration is sort of core to how spring operates, and annotations are no exception to that.
And then if you want to change a value at runtime you have to restart the executable?
Would be nicer if we could handle creds like it wasn't 1992, but this does the job too.