I realize that roans change seasonally... what I found interesting is that you couldn't see this colt's spots at all for half the year. He looked like a roan QH.
I know many other Appies that look nothing like their foal photos.
One of my family's fillies was born a solid black (only one dime sized white spot on her hip... and a sock) she's now a mostly grey horse with black spots. She has no grey parent - so she's not grey at all. She's getting more spots every year and she's getting more white hairs too.
We have a gelding here who was born a really classic rich bay with blanket/and spots - he's slowly turning leopard (in looks), which is what his mother did as well. In the process he's kept his black points (so still obviously a bay) - but his body coat has changed in some areas to a interesting shade of red and you can see the emerging spots underneath in that darker brown (bay) color he used to be.
I've seen many other cases where the Lp gene causes the coat pattern to change so much you wouldn't know it's the same horse... which is why I suspect something similar is going on in the OP's case.