So, if I understand DF correctly, then the engine is just bad.

Digital Foundry video sounds fairly positive on the PC port with annoying resolution fullscreen bug + low res pre rendered cutscenes been the big issues, 980Ti at 1440p on max setting without AA holds 60fps.

It's a poorly optimized port for damn sure. It also runs in a trend that a good number of Japanese releases have on PC, menu options are limited. Likely because there's not many people working on the port when it happens. Dunno if it'll see lots of patch support in the future, either.

That's really strange, the game has very positive reviews on steam and a pretty good user score on metacritic, usually when a Pc port is bad that doesn't happen at all, are you sure is that terrible?

What I gathered from reading the user reviews on Steam is that most of the negative ones on performance are those with 7xx or weaker 9xx graphics cards, The DF video says the performance isssues are more to do with the engine and are there on the PS4 versions also.

So is not a terrible port at all, the OP is pretty missleading, I have seen the digital Foundry video and they clearly say that as long as you have the hardware PC version offers the best experience, that hardly sounds like a terrible port. 

I'll leave it here.
http://www.dsogaming.com/news/modder-has-figured-out-a-way-to-almost-double-the-performance-of-nier-automata/

Quite embarressing, don't you think?

Yea well, if its not achieving 60fps on the ps4 pro, it won't achieve 60fps on a 960. It also runs at 1080p on a ps4 pro instead of say, 1440p checkerboard like most other games so... Its pretty easy to see why you would have to turn it down to a medium in order to achieve 60fps since a 960 is closer to a regular ps4 in terms of performance than a ps4 pro. From what I hear, the high settings on it defaults to 8x MSAA which is very demanding. So anyone trying high preset should really turn it down to 4x MSAA or lower.

The port, while not the greatest is certainly not really that bad when you are considering how the consoles are performing. This isn't a PC only issue when the ps4 pro which runs games like Horizon at 1440p+ smoothly only manages to run Nier at 1080p. So considering that, the performance you are getting with a 960 is pretty much on par with what people should expect considering how its performing on consoles imo. There are of course, some bugs which do need to be fixed.

Is it bad just a weak port or bad like Arkham Knight?

Not even close to AK.