It took me a couple of days to find out what was causing it, but I ended up being able to “fix it” with one line in the UndoUtility of CanvasCore.

The issue

Whenever I recompile scripts, all my scenes get set dirty, which is driving me up the wall.

The cause

Since I have a complex scene setup, I expected all kinds of culprits, like Layout Groups, Aspect Ratio Fitters, etc. I’m pretty sure there’s a Unity issue deep down in there still. But replacing them did not do the trick. Somehow, Unity’s LayoutRebuilder’s PerformLayoutControl got triggered, when scripts get recompiled, which targets ILayoutSelfController and others and causes UI objects across the whole hierarchy to become dirty.

PerformLayoutControl, in turn, gets triggered by Unity’s Undo system. RegisterCompleteObjectUndo, specifically (and others). And this call I found in CanvasCore’s UndoUtility (RecordObjectComplete).

The fix

Given that it’s called from all over the place, I figured EditorApplication.isCompiling would do the trick, but it happens just after compiling, so it’s already false. EditorApplication.isUpdating, however, is not.

So adding
if (UnityEditor.EditorApplication.isUpdating) return;

seems to do the trick.

Conclusion

It’s likely that this issue is not reproducible in a simple scene. I’m pretty sure there’s something wrong with Unity’s layout system because, without UI things, it’s not an issue.
Nonetheless, it’d be awesome if you could include this fix in future versions, so I don’t have to go looking for this issue all over again once I’ve forgotten all about it and update NodeCanvas.

Thanks!