Hmmm…Yes a headtube facing tool seems like a reasonable option to remove a few mm. What about trying a longer stem…this would get you more reach and get you lower down. Also some handlebars have lower drop sections than others, and so that might buy you a few mm as well especially if you like to ride in the drops. I hope you figure out a way to get everything suited to your liking.
SB
Good thing about the EU is that it takes consumer protection very seriously. There is the European Consumer Centre (ECC) Network, which provides advice on your rights, given by lawyers, and can also help settle disputes with the seller. That service is free, it is funded by the EU. See European Consumer Centres Network - ECC Net - European Commission
I was in a similar situation a few years ago with a custom ordered product that didn’t meet specifications. The seller was similarly unresponsive, insisting that nothing is wrong and only offering that I can ship it back at my cost to have it assessed by them. Only when I told them that I have contacted ECC and that one of their lawyers may be in contact with them, their tone changed completely and we found a good solution.
From what I remember, there are EU regulations that if the product is not as agreed upon, they need to do one of the following: (a) repair (if possible), (b) replace (if within reason), or (c) offer a discount. It depends on the individual situation which solution is reasonable. In your case, the same fit can be obtained with a different stem, so repair or replacement might be unreasonable due to excessive cost of shipping it back and forth. But you should at least be entitled to a discount.
Disclaimer: I’m not a lawyer, this is my layman’s opinion based on similar experience. I may recall the EU regulations incorrectly.
Otherwise, I can only agree with what others have said. Try it, see if the position works for you. And if not, try another stem or remove spacers to get a similar fit to what you intended.
If the legal route is chosen, I suppose the question becomes, do the fork and frame match the agreed upon drawing? Does the frame measure to the drawing?
This seems like a very interesting route to consider. Great to hear that it worked for you. I have actually already contacted Pegoretti with those requests based on EU law: repair, replace, refund or discount. They have not even addressed them, instead claiming that the frame needs to be assembled by them in Verona to magically reach the specified numbers 
I was not aware of the ECC. Thank you!
Yes. My original question in the post was: is the drawing correct in the first place. For sure we can see there is a 3mm mistake in the drawing regarding the headset top part stack. This is an undisputable mistake on the designer’s part. A couple commenters earlier suggested there might be something with their calculation of fork length vs. A2C, but this seems unconfirmed. Secondly it would be a question of whether they built the frame correctly.
That Darimo stem is -25° or more. Your head tube angle is 73°. A -17° stem angle would place the extension horizontal with the ground. A -12° stem would still angle slightly up relative to the ground.
With a 73° head angle, a -12° stem would be parallel to the 5° sloping top tube, which should actually look really nice.
Late to the party here. Firstly, I think the advice you’ve gotten to try to deal with it is solid. It’s super disappointing to have to deal with errors in such an expensive frame, but unfortunately they don’t quite build tolerances when you buy the frame. +/- a few mm is pretty reasonable and it seems like with component dimensions being wrong that’s about the range you’re in. I’ll +1 the suggestion to just get a stem with more drop.
Also, as other have said, that very much looks like a bikecad drawing and you’d have to be very….talented to get the calculations wrong with it. Though that doesn’t guarantee the dimensions were translated properly to the frame
As for the root cause, I didn’t see if anyone mentioned measuring the frame. The headtube is listed on the drawing. And eyeballing the CAD vs the bike picture either the head tube is too long or the top tube was mounted a bit low (which could have implications for the TT length/reach). It’s also possible the BB drop is wrong which could make the stack/handlebar drop be off, so you could check that. All of this depends on what their jig setup is like and how they cut their tubes, but it’s possible the jig was setup a little incorrectly.
This was sort of my thinking. If the frame measures to the drawing and that’s what was contractually agreed to, they may just say we built exactly what you agreed to. They may claim the bits are out of their control.
Thanks. My intention was to first look for help in verifying the drawing, because that is hard to dispute. Like the identified mistake in headset top part stack. Then absolutely the actual frame measurement. My mechanic and I did measure it and the tube lengths look correct, although it is difficult to measure very precisely. One thing I did not focus on very much is the bottom bracket drop, which you mention, which definitely would influence saddle to bar drop. It seemed fine, but I will try to measure it again as precisely as possible.
Keep in mind that the saddle-to-bar drop is also in the drawing. I believe by including that they guaranteed it.
You can best measure BB drop without the front fork. Get a digital angle measure. Position the frame on a horizontal surface. Support and lift the rear of the frame until the seat tube has the angle that is on the design page. Measure the height of the center of the rear axle and of the middle of the BB tube - the latter can also be calculated based on the diameter of the tube.
With the frame in this position, you can also double check things like the head angle…