Hi @aislas, thank you for including the images.
We have recently improved this case in the latest version of the Revit plugin and the Model Editor V2 which removes the need to adjust the extrusion height for the windows to show up, as long as the top exposed is set correctly. Try downloading the latest version, and switch to V2 and the problem should be resolved. See here for the announcement: We Didn't Make it to AU, So We're Releasing the Model Editor V2 for You Instead
If you want to stay in the current version of the Model Editor, you only need to change the height for the rooms with windows on top instead of changing it for all the rooms in the model. That should address the issue that you mentioned here.
Let me know if you have any other questions.