Well at least (a) (the user configuration) should be part of the domain.xml. So that all nodes in a domain not only have a consistent configuration, but also activate the same services - regardless of -c. This is why it is important that all our deployments are moved to a common repository.
(b) is a bit different. The server side configuration more represent modules, which are available in a repository and shared across multiple domains. Ultimately this has to move to a domain level, where we can use a provisioning service to provide the appropriate version of the module for a domain. Where different domains might have different versions of modules.