My 1090 and 1190 both do this, neither have significant warp in the discs.
On the internet there are a number of theories including pad material gets stuck to the discs, my 1090 was quite bad and a few minutes with some wet and dry improved it a lot, when the weather draws in I will take the brakes off and clean everything up, scuff up the pads with a wire brush and give the discs a more thorough clean and I think that might work.
My guess is KTM know what causes it but won't say, there are certainly a lot of people this has happened to. They will only replace discs if they are out of true, and I suspect yours won't be, although badly pulsing brakes is still a fault IMO regardless of if the discs are warped, but I doubt you will get anything done about it - but still worth complaining to the dealer, you might get lucky.
If the clean-up sorts mine out and it then comes back I will just try some different pads.