Since the issue with the scratching wiper arm and colliding domed nut more and more sounds like an issue with the bonnet, some more detailed measurements were made.
With the bonnet closed, the distance from the glass (at the edge of the visor) to the bottom of the bonnet is 40 mm:
Attachment 14587
.. from the glass to the top of the bonnet: 45 mm:
Attachment 14588
The values should be 45 and 50 mm, respectively, which gives a sufficient clearance of about 5 mm between the domed nut and the underside of the bonnet (like stated previously).
Now, contact to my local and experienced body shop was made. They stated that it's possible to bend the bonnet into shape but it's high effort and risk - they would only consider it as a very last resort.
While talking and explaining the situation, it was observed that the required clearance can be obtained without permanently bending the bonnet - hence the idea to support the bonnet from underneath in such a way that it's kept in a proper shape while being closed. For testing purposes, two improvised rubber mounts where put on the sheet metal holding the weather strip:
Attachment 14589(the rubber domes should probably be more close together)
After closing the hood, this resulted in a clearance of 43 and 48 mm - almost according to spec :)
The tricky part is how to combine this with the cowl cover and the weather strip - ideas are welcome.
Attachment 14590(not like this obviously)