I got your point now , that actualy happens if you palce any file that does not support layers like jpg or png,
Here is my workflow as I run into this issue and I solved it my way to work non-destructively:
whenever I palce any file ( jpg , PNG , ... ) it will be placed as smart objet, the first thing i do is converting that smart object again to another smartobject ( i create a shortcut to for that ) now when you double click on that smart object you will get inside the smartobject and you will be able to wotk and save without getting the message to flatten your artwok because the new smart object will be saved in "psb" format.
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