Thanks for posting in Microsoft MECM Q&A forum.
Per my experience, when you set both option "Pre-download content" and "Run another program first", it will only pre-download the program you want to run first rather than all the content. Here is a uservoice for about this:
Fix Pre-Download when using "Run another program first"
You could also submit a new uservoice in Microsoft Endpoint Configuration Manager Feedback:
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