In my web map, the scale is roughly 1:50,000 (best guess). An experience builder app that uses the web map appears to be automatically zoomed out at roughly 1:75,000.
Why is the zoom level in Experience Builder different from the web map?
Related idea: Honor web map scale/zoom in Experience Builder
I've noticed this too! It's annoying at times. For example, if you set up layers in a web map with labels, and set the visibility scales for multiple label classes, when you view the map in ExBuilder they don't draw how you set them up in the map.
You're spot on though, the scales do not line up, and it affects how everything draws between the two (map vs app).