Yes, Their seperation is much further along. Unlike Dogs goldfish can have 1000s of offspring per year so they were able evolve faster from the carp than dogs could from wolves.
Wolves and Dogs are still pretty much genetically identical while goldfish and carp are a much further apart, For example Goldfish have 94 Chromosomes while the Carp has 100. Unlike Dogs and wolves which can still produce fertile offspring of both sexes goldfish-carp hybrids can only produce fertile males. The genetics of the Carp family of fishes is very bizarre and unique, Different species (Even of different geneses) can breed that way also, There is a lot of redundancy in their genetics (hence the high Chromosome #) which enables them to produce hybrids this way so using the strict definition of speciation of being able to breed with each other doesn't apply in the case of Goldfish and Carps. Though that's only with the common goldfish and carp, I am not sure about the fancy breeds (the ones at the bottom) if they can still mate with Carps in many cases they can't mate with other breeds of goldfish and produce viable offspring (Not because of genetics but because their body layout is different that their offspring's swim bladders get screwed up so they die)
What do you mean with "New ... Organs and structures" ?
Well look at the bottom 3 pictures, You won't find a bubble eye (#2) or the lionhead/oranda (#1 & #3) head growth on any carp, These fancy breeds also have 2 tails and their body plan is egg shaped as opposed to the cigar shape of the common goldfish and carp and their swim bladders are arranged differently. And in picture #1 notice the scales, Those are called Pearl scales which are a unique type of scale that you also won't find on any carp or any other fish.
And since you don't find these features in the wild carp and the ancient Chinese didn't have genetic engineering capabilities we can safely conclude that they arose from mutations and through selective breeding they evolved. And yes even though people selected the breeding it's still evolution, Those that had unique features that piped it's owners interest survived and got to breed while those who didn't became dinner. And before you say they were always there but not seen because those features wouldn't survive in the wild, The bubble eye was first recognized in the early 20th century so for it to have remained hidden for the first 900+ years and hundreds of generations of domestication is a ridiculous notion (And other features came way later also).
I don't know the exact number but I would bet that goldfish (especially the fancy breeds) are further apart genetically percent wise from their original carp ancestor than chimpanzees are from Humans. I could probably name more differences between goldfish-carp than humans-chimps. If not they are pretty close in separation differences and if in 1000 years goldfish can desperate that far from their ancestors in 5,000,000 years humans and chimps could from theirs.
Make that
if goldfish can separate that far