Sending, receiving, and organizing email in Outlook.com
I don't know what version of Outlook desktop you are using but both in the initial rule creation and in step two above, the only option is to apply / run it against the Inbox. There is simply no other option displayed.
I'm using Office 365 Outlook Version 2407 build 17830.20138 Click-to-Run.
I have found however, if you manually run the rule later, it will allow you to run it against the Junk folder. I added "Run Rules Now" to the Quick Access Toolbar which helps a little, but you still need to select the rule and select the Junk folder.