Hello Lauren,
Appreciate for sharing the detailed information and per the description, I understand your concern and we can see the same behavior at our end, the reason behind not showing values for the items with multiple values is explained in this article: Incomplete search results for choice type columns with multiple values (though this article explains about the SharePoint 2013 the search mechanism is also same with SharePoint Online).
As a workaround, you can refer to the steps in the thread: How to search choice field values with 'Allow multiple selections'
Thanks for your understanding and patience. Have a good day and stay safe!!
Best Regards,
Chitrahaas