When I exported my game objects applying transform before opening export window I did not change any preset in export window, there was no problem about scale and rotation in unity.
But in these days it does not work. I have to always select “Apply Transform” option to fix it anymore.
Odd. maybe play around with your Up and Forward settings. I know other software’s like unity doesn’t follow the Z Up rule that Blender uses. but I feel like you may be able to fix your problem
i was spending a significant amount of time on this and found configs that are working for me. Maybe you have success with this as well.
Here are the presets for the blender export and for the unity import:
You can add the FBX import preset with the preset manager in the project settings so all your fbx files will be imported with these settings
When testing how the transformation arrives in unity make sure you delete the object from unity’s Hierarchy and Assets and re-add it. If you just re-export after changing the export/import options it will do some strange stuff with the transformations.