Peter,
the lip does not interfere in any way with the window mechanism and can be cut back.
Looking at your test holes I am not sure whether the mirror will be far enough back so that you can see it completely when sitting in the driver seat. I am not sure where this "1-hole further back" instruction originated, imo it is not enough.
Take the threaded stubs out of the mirror and then have a helper put it flush on the door and check whether it is obstructed. Make sure that you have the outside chrome trim installed to know how far the mirror can be mounted up on the rim.
If you look at the photo in my Pagodentreff post you'll see that I used a second reinforcement plate in my 1966 230SL (now sold). That particular style is NLA and the current ones are thicker. You should reinforce that thin skinned aluminum door.
Here is a photo showing the plate in my 1964 230SL. The lip on these early cars extended even more forward than on later cars and this area is different from yours.