The SpringEmbeddedCacheManager contains the following comment:
A user may further customize the SpringEmbeddedCacheManager's configuration using explicit setters on this FactoryBean. The properties thus defined will be applied either to the configuration loaded from Infinispan's configuration file in case one has been specified, or to a configuration initialized with Infinispan's default settings. Either way, the net effect is that explicitly set configuration properties take precedence over both those loaded from a configuration file as well as INFNISPAN's default settings.
In this current version, setting a configfile + overriding properties does not seem to be possible. This can also be seen in AbstractEmbeddedCacheManagerFactory.createBackingEmbeddedCacheManager(), where the overrides are only applied iff configurationFileLocation == null.
I made a little workaround to fix this issue, but it's a mess because the DefaultCacheManager does not seem to allow overriding values if it gets its config from an InputStream. The workaround is available at https://gist.github.com/MikeN123/5618297
It seems the same issue exists in InfinispanNamedEmbeddedCacheFactoryBean, there configuration overrides don't seem to be applied if configurationTemplateMode == DEFAULT, or configurationTemplateMode == NAMED, whereas the documentation says that should work.