My understanding is that it's not exactly true that goat's milk is naturally homogenised. However, it's really kind of a technical nitpick. Milk fat is contained in "globules" (that's the technical term, believe it or not). The globule has a membrane that keeps it intact. Homogenisation breaks that membrane as part of breaking apart the globule. Goat's milk have very small globules, which is why the cream doesn't rise (it's not prone to sticking together into large structures and rising to the top). Some manufacturer's do, indeed, homogenise goat's milk even though it is meaningless from any practical standpoint. Why? Sigh... because the milk industry sucks (as far as I can tell).
Some places actually have rules that milk must be homogenised. This is not from any consumer protection perspective -- it's 100% a play by large milk pools to economically force smaller producers to pool their milk. It increases the capital cost of producing milk and prices it out of the range of small producers. It's scummy and awful. Ontario, Canada actually had a law (that I think has now been relaxed, but I haven't checked for several decades so I'm not sure) saying that non-homogenised milk could not be sold in quantities less than 25 liters. The 25 liters was so that commercial cheese producers could buy non-homogenised milk, but that the public would be unable to do so (and hence farm gate milk sales would be all but impossible). Interestingly, the legal definition of milk was so precise that when "organic milk" was starting to become a thing it turned out that it could be sold as something other than "milk". So for a while, you could buy non-homogenised milk if it was from an organic producer. The milk lobby got to work and closed that loophole pretty hard -- the forced all organic milked to be pooled into an organic milk pool "for the safety of the consumers".
I hate the Ontario milk industry with a passion, if you can't tell. They were the worst -- of course it's been a long time, so I'm not sure what the situation is now. But this is almost certainly why you are having trouble finding non-homogenised goat's milk. Bloody business people and their need to grab a share of everything.
What we really need is a movement similar to the "Real Ale" movement in the UK. "Real Milk" -- pasteurised, non-homogenised milk should be the minimum a consumer can expect. If you *want* homogenised, fine (some people like Euro lagers with 40% corn too -- I'm not going to stop them). I'm sure there are dairy farmers who would come on board.