Hello All,
We have an official bug (BUG-000128447) with reproducible steps that result in layers not clipping properly in the exported result. The key finding is if the last layer in the draw order has any transparency.
For example, here I have a map where the last visible layer in the draw order has transparency. Only the "Clip Layer" (blue outlined polygons) are excluded from the clip.
I export and nothing seems clipped.
Note that the last visible layer is "BUG----Transparency". If this layer is moved in the draw order so that it is not the last visible layer the features are clipped in the export as expected. In the example below I've moved this layer above "Clipped Layer".
In cases where you want/need the layer order unchanged you can add a non-transparent "placeholder" with no symbol and place it the bottom of the draw order. Make sure that it is tuned on.
Export result.
This is one scenario that we know, and more importantly, can reproduce, where clipping is not working as expected. If your scenario/draw order is not similar to that outlined above, please contact support at https://support.esri.com/en/contact-tech-support.
Hopefully, this information can help you all move forward with your work.
Tom