The chestnut in Haffies is probably easier to explain - because chestnut is recessive, and horses need two red genes to be chestnut, they only have red to pass on. So breeding two chestnuts will only ever give chestnut - kind of like my Welshies.... four liver chestnut mares, if put to a chestnut stallion, would only ever produce chestnut foals - so if we were working with a very small gene pool, with a lot of chestnut in it, it becomes easier to see how a breed can become chestnut and nothing else.
Dun is a strange one... especially in Fjords where they have a full range of base colours as well. Dun is dominant, so a horse really only needs one dun gene to be dun - so it's a lot harder to see how a breed can become homozygous for a gene like that.
But.... Prezwalski's horses are all dun too, so it's not unique, and they are really as close to primitive horse as we can get - so we can assume that their colouring is also as close to 'original horse' as it's possible to go. Studies of wild horses left to breed without human intervention have shown that dun characteristics actually 'develop' even where there was no dun to begin with, showing that dun is what's called an 'atavistic' colour pattern. So... dun is, it seems, a lot more complicated than just one gene. It could be that dun is a kind of 'default' colouring, to which horses would eventually revert if left alone to breed - a kind of reversal of breeding for colour.
Perdita - fleabitten is the very last stage of greying, although not all greys go fleabitten. The freckles do tend to be of the same colour that the horse is underneath the grey - I knew a fleabitten gelding called Robbie who had dark brown flecks all over him, and he was born bay (he had so many that from a distance his body looked roan) and I think Mehitabel's Petal is fleabitten now too. May is also developing little orange flecks - not many though, and she's 11 this year, and she was completely white at 6. Not all greys do go fleabitten, some get masses of freckles, others just get a handful.
The other marking that white greys can get (especially those with Arab blood) are blood marks - big rust coloured patches usually on the shoulder. They develop after greying out is done too, and start out as small marks which get gradually bigger.