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There are two ways of updating your cluster settings.
Cluster configuration. You can create Cluster Configuration. Follow documentation for which properties you can update in custom config. This will trigger rolling restart of the cluster.
Dynamic Configuration. This option allows you to use kafka-configs CLI command to update configuration at broker level. You need to have access to the brokers in you VPC or via public access. Once you issue a command, config will be applied without the need to restart the broker. Note, not every config can be changed on a broker level. Most of configuration needs to be done FOR EACH broker separately.
Also, please note, you cannot have an access to the file system at all, but you may use Kafka Admin APIs or AWS APIs to execute config updates.
You can connect using the methods in the following documents.
https://docs.aws.amazon.com/msk/latest/developerguide/msk-connect-getting-started.html
Or you can enable public access and access it from your own PC with a client.
https://docs.aws.amazon.com/msk/latest/developerguide/public-access.html
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Despite I cannot have an access to MSK file system, is it possible to config server.properties using AWS API? I would need to upload OPA plugin for Kafka (a ZIP file), and then specify its utilization in server.properties config file.
since you don't have an access to the file system, you also cannot upload any JARs or other artifacts/files to the brokers. MSK is fully managed environment. In other words, you cannot use OPA plugin. Instead, you can use PLAINTEXT and SSL (with mTLS support via AWS Certificate Manager) as provided authorizers.
Thank you for your answer I will use another option instead ;) Maybe AWS will one day implement OPA as an auth option!