How to tell the PCB DRC that the connector is in fact a wire?

[Piotr]

@MustardMan

but left out of the gerber pack (it does make creation of a ‘gerber pack’ a lot more difficult and prone to error though).

I was thinking 10 minutes and I can’t get what ‘difficulties’ in creating gerbers you have in mind. When 15 years ago I had to add at 2 layer PCB 3 wire connections I just changed design into 4 layers and draw 3 tracks at one of extra layers.
Then when generating gerbers I just didn’t checked internal layers to be generated. Done.
But not checking 2 layers can’t be said to “make creation of a ‘gerber pack’ a lot more difficult and prone to error” so I wonder what you can have in mind.

@devlaam

Too bad, i really hoped i had overlooked something.

You overlooked that you can add extra layers and make there connections just to silence DRC.

@devlaam

In order to produce it in one go (cheaper) it is designed as one PCB that is to be manually separated after production.

Typically there are no imposed by the manufacturer rule that your PCB have to be rectangle. You can have any PCB shape. To make separation easier modify Edge.Cuts to have most of work be done by PCB manufacturer.
Here I showed the example of KiCad 5 made PCB I ordered 4 years ago:

Panelization for complex edgecuts

Different shapes are not the big problem. Here is how I have once (with KiCad V5) done one my prototype so then I could order it as single PCB: [A38_All] And some details: [A38_detail] I use 2mm gap between PCBs. The rest if needed you should be able to measure from picture.