Based on my understand of the issue. Continuous Job runs on all instances that the web app runs on. Indeed, you can optionally restrict the WebJob to a single instance (different in your case).
Note that App Service will only look for a script under the root directory of that job (not under sub directories of it). Only these are supported file types for scripts or programs are listed here:
Laravel, uses the public/ subdirectory as the site root.
Jobs are deployed by copying them to d:\home\site\wwwroot as illustrated below. These Jobs will run under the worker process of the SCM\Kudu Web Site and not the main site.
Path : wwwroot\app_data\jobs\continuous{job name}).
To set a continuous job as singleton during deployment then you can simply create a file called settings.job with the content: { "is_singleton": true } and put it at the root of the (specific) WebJob directory. However, in your case { "is_singleton": false }
If your requirement fits you can use WebJobs API or Azure Functions