Code in org.jboss.as.connector.subsystems.datasources.AbstractDataSourceService.AS7DataSourceDeployer#setMcfProperties(..) never inspects org.jboss.jca.common.api.metadata.ds.TimeOut#isSetTxQueryTimeout().
org.jboss.jca.common.api.metadata.ds.TimeOut#isSetTxQueryTimeout() is not inspected elsewhere, so org.jboss.jca.adapters.jdbc.BaseWrapperManagedConnectionFactory#isTransactionQueryTimeout field is always false, no matter what configuration is.