Let's remember that shinies are a game phenomenon. In the actual world of pokemon, you do see greater colour differentiation. Pinkin Island pokemon are not shiny yet are pink. Pokemon native to the Orange Islands occasionally have a more tropical look to them (search that yourself if you need pics). Then we've got that grossly overrated Pichu. There's surely more examples I'm missing...
So how do some shinies have minute differences like Gastrodon, Happiny, and Garchomp while others are much more different? Let's look at Project R...anyone recall this? You'd better since we're returning to Johto. It was the codename for TR's plot at the Lake of Rage. They were testing radio signals to "control" pokemon, and the result was a prematurely-evolved Magikarp where the Gyarados had more Magikarp-esque colours. There's no use debating that that Gyarados isn't shiny; it had the shiny bling in GSC.
Clearly, shinyness can be induced by unfavourable exposure to forms of radiation. Excess UV radiation exposure might lead to the Orange Archipelagos' off-coloured pokemon, while other forms could lead to what we know as shinies. Take a look at Cradily. It retains is Lileep colour just like Gyarados and the Magikarp colour (again, roughly).
However, I know someone will point out that not all shinies follow that pattern. Some could easily be the result of, simply, location. There's more than one of every shiny but not enough to go 'round, so I'll label them all as endangered species. If you've got a population of Tropius that strays from the densly-forested 120-Fortree area to the beaches by Lilycove, then (assuming they don't return), over a long period of time, they'll take on a more yellowish colour to fit their, uh...beach habitat. We could play this game all day. Grimers go green due to living in different hazardous substances as opposed to the usual "sludge" which happen to have the same colour as them. I would not be surprised at all if there are blue and brown Grimers, too.
It doesn't necessarily explain Golem specifically, but it's a start.