I just noticed this, too. I cannot find a suitable alternative. Please at least adjust the help-text to tell users what to do instead.
The main issue for me is the fact that Jenkins even triggers builds on branch-indexing when the build is parametrized. Of course, without parameters, these builds usually fail.
I know that the option is deprecated, however I am sorta stuck. We are using Github Organization type jobs and are trying to run "master" branch builds nightly instead of continually. I see no clean way to implement this with the current API.
Even I am facing similar issue. I have disabled GitHub WebHook that points to Jenkins Server because I want GitHub WebHook to point to a Lambda function. My lambda function filters Webhooks events and only when a specific comment is made on a PR I want to trigger a build on Jenkins. Unfortunately, after disabling the Webhook that points to jenkins directly, PR branches aren't being discovered and hence I am unable to trigger build on PR branches. I can resolve this problem by re-enabling the GitHub WebHook that points to Jenkins Server but disabling "Suppress automatic SCM triggering". Unfortunately I can't find that anymore on Jenkins Configure due to updates. How should I go about? I want Jenkins to discover branches but not trigger builds on its own.