The problem arises when more than one application wants to use the common code but for different target environments. Application1 wants to target DatabaseA while Application2 needs to target DatabaseB. I'm all for having a default configuration of beans provided in the libraries to ease integration with applications with appropriate reference documentation to understand the bean configuration and how to replace it. IMHO this is something that helps make Spring stand tall in the field.
However when a default configuration gets injected with a resource bean (eg: a DataSource), for an application to use that configuration with a different resource (ie: a DataSource pointing to a different DB) then the entire configuration has to be copied and pasted into the application context and jiggled around so that the correct resource bean is injected at ApplicationContext boot time.
Ugly and painful!
What should happen is that a resource factory bean should be specified in domain libaries, with applications providing their own implementation.
Fortunately we're Agile, so it shouldn't be too hard to clean up.