It looks like a tricky problem. When I am faced with such problems I try to exhaust options before altering original parts..
With that in mind, I would look for a button head (rounded top) screw to replace the hex-head that hold on the derailleur hanger to see if the lower profile of the button head gives you the needed room to mount the fender in its designed configuration.
If that does not do the trick I would weigh my options between the fender angles you mention (hard to comment on effectiveness not seeing pictures) and perhaps countersinking the derailleur hanger so a flat head screw can be used to buy you the clearance you need.
Final thoughts... the derailleur hanger hex head looks pretty beefy. I have seen them attached with a couple 2M screws which are quite small. Changing the screw to button or flat head will result in using a smaller hex wrench for tightening. If getting the required torque to tighten it securely is a concern you may want to consider using some medium strength lock-tite as a measure against potential loosening due to vibration.