Where I work, we've used collection properties (collectionprops.json) to store collection specific synonyms & query-elevation configuration. We have custom plugins for those features to read/expire this information in addition to implementing other custom requirements. It's somewhat of a hack but it works while being rather lean implementation-wise as it uses an existing mechanism.
It'd be interesting if a collection could have a configset overlay as a general feature and for modifying anything. It'd be stored inside a collection's ZK node tree. SolrResourceLoader would overlay this with the backing (ConfigSet) source.