@DrunkenMastah thanks for the pointer.

I modified the class to my needs, just throw it into an Editor folder. It will log warnings when there is something dirtying the scene <1 second after saving it:
https://gist.github.com/krisrok/eaa8b227b62e19555c5aefe86c5b6618

Also caught by this 2019.4.5 and can't get the workaround working. I now cannot use a plugin that searches for references (AssetUsageDetector - a VERY useful tool) as it requires you to save the scene before it starts - and when you do it marks it dirty and so the tool thinks I haven't.
I really hope Unity notices when a bug report is still getting comments that now are more than 2 pages. Surely a basic flag that users are not happy.

Can we get the reasoning for the decision not fix this? Is the fix too complicated?

After searching the forums I came across this little post by
arelian11 · Feb 05, 2015 at 10:29 PM

https://answers.unity.com/questions/801464/get-dirty-state-from-a-scene.html

Workaround Solution:
Attach this to a game object in your scene and save the scene.
Now every time you compile and if you scene is marked dirty it will be detected by this code and logged.
Click on the logged line in console and it will point you the offending gameobject that is marking the scene dirty.
Next, check the parent of the target game object of grandparent or so on...and if you see that it has a scroll rect, fix the floating values on the scroll rect to be rounded integers instead of floating values.

This will fix the bug and the scene won't be marked dirty anymore.
My scene had 30 or so objects that had this problem fixed it in 5 mins. No more version control bloat and more problems in sharing scene file.

<code>
public class SceneDirtyFlagChecker : MonoBehaviour
{
private static bool sceneIsDirty;

static SceneDirtyFlagChecker()
{
Undo.postprocessModifications += OnPostProcessModifications;
}

private static UndoPropertyModification[] OnPostProcessModifications(UndoPropertyModification[] propertyModifications)
{
sceneIsDirty = true;
Debug.LogWarning($"Scene was marked Dirty by number of objects = {propertyModifications.Length}");
for (int i = 0; i < propertyModifications.Length; i++)
{
Debug.LogWarning($"currentValue.target = {propertyModifications[i].currentValue.target}", propertyModifications[i].currentValue.target);
}
return propertyModifications;
}
}
</code>

2018.3.6f1 same issue. ScrollRect is causing it. Source control is bloated. Workflow is bad. How is this a Won't fix?

Why is this a Won't Fix? It's extremely frustrating and like others have questioned, is this behavior OK?

Also happening for me in 2018.3.0f2. As per BCook99's comment, this is annoying when using source control

This is happening in 2017.2 as well. WONTFIX? Lame!

A workaround for this is to identify the component that is making your scene dirty (in my case a ScrollRect), disable in the editor, and enable on Awake.

private void Awake()
{
GetComponent<ScrollRect>().enabled = true; //disabled in editor as per unity bug
}

If anyone in Unity reads this, it would be good if you care about at least giving a workaround when you mark something as a "Won't Fix", consider the person that logged the issue spent time figuring our what was going, it was thanks to that person I found that my ScrollRect was the problem.

Same issue on 2018.2.3...