In current implementation of hibernate-infinispan we can tune only entity and collection settings via hibernate.xml.cfg. But tuning in same way for queries needed too. In current version there are always the same cache region for all queries (look at org.hibernate.cache.infinispan.InfinispanRegionFactory.buildQueryResultsRegion) and it's incorrect.

In org.hibernate.cache.infinispan.InfinispanRegionFactory.buildQueryResultsRegion
Replace those lines:
String cacheName = typeOverrides.get(QUERY_KEY).getCacheName();
CacheAdapter cacheAdapter = CacheAdapterImpl.newInstance(manager.getCache(cacheName));
To:
Cache cache = getCache(regionName, QUERY_KEY, properties);
CacheAdapter cacheAdapter = CacheAdapterImpl.newInstance(cache);