Disabling command-eval also disables plugins

When running agents on v3.8.4, we were using these settings

```
BUILDKITE_NO_PLUGINS: 'false'
BUILDKITE_NO_COMMAND_EVAL: 'true'
```

This allowed us to run plugins (we have our own security check in place for plugins), whilst also disabling command eval.

According to the documentation for command eval https://buildkite.com/docs/agent/v3/securing#disabling-command-eval this shouldn't have been possible. This is backed up by https://github.com/buildkite/agent/issues/674

In any case, we were indeed able to run plugins with command eval disabled just fine. However upgrading to 3.9.1 has broken that functionality.

Can we get some clarity if it was working incorrectly before and that "bug" has now been fixed (so we need to find a new way to disable command eval), or should it be that way and the documentation is misleading?

Start with the command-eval documentation at buildkite.com/docs/agent/v3/securing#disabling-command-eval and compare the BUILDKITE_NO_PLUGINS and BUILDKITE_NO_COMMAND_EVAL settings across agent versions 3.8.4 and 3.9.1. Confirm the intended plugin behavior when command eval is disabled, then update the behavior or documentation and add coverage for the reported configuration.

Written by the indexing model from the issue text.