You should not have 1 job with different behavior. If you need other behavior, customize the work for the behavior. The best bet in your case is to have 2 separate tasks, one for assemblies built using SCM and one for manually built assemblies.
There is a plugin that allows you to filter tasks on separate pages (at the moment they cannot remember the name). You can install all SCM assemblies on 1 page, and manually on another, and then configure the manual assembly page as the standard entry. Users will only see jobs that you want to run manually by default, but you can still access the SCM assembly by selecting a different page.
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