As you mentioned certain cli tools are marked not to be supported, for your requirement being the kafka-server-startup and shutdowns scripts. It is not guaranteed that the manual setup initializes the context of Kafka the same way, as Cloudera Manager would. While it may work for the restart but there are environment scripts and some other process management that Cloudera Manager does. Hence, when you restart using Cloudera Manager there would be uncertainties on the state of the process.
As you said you have problems accessing the Cloudera Manager UI, you can also use the Cloudera Manager API for your requirement.
https://docs.cloudera.com/documentation/enterprise/6/6.3/topics/cm_intro_api.html
SME || Kafka | Schema Registry | SMM | SRM