The biggest two issues are predatorproofing and dust.
All things being equal it is usually easier to predatorproof a freestanding coop than a section of a barn. Of course it can be done, I just mean you have to be extra careful about it
Do not neglect the rat issue, nor spaces up near the rafters, nor wee gaps that rats can chew through or weasels can, er, weasel through. (Weasels are most places in the continental US, even if you have not SEEN any)
As far as dust goes, I do not know how sensitive goats are, and of course the more open-air your structure is, the less dust there will be. But if this is basically an enclosed barn, it would be smart to at least have a good plan B in mind in case you discover you really need to close off the chicken area from the rest of the barn (goats, hay storage, etc). In particular you prolly want the chickens as far as possible from the milking area. It is great to be able to ventilate the coop into the rest of the barn as well as to the outdoors, just make sure it can be closed down or off, you know?
Good luck, have fun,
Pat, who really really wants goats but has no practical justification for them so is just waiting til the kids reach 4H age... LOL