I do have experience with this so I can tell you that guaranteeing less than a minute is talking out of your ass. It's not hours per pokemon, but it takes a few minutes at least to do it right, but then there's a lot of them to do. It adds up and there's other things to do with their time. So what do they do? Make an algorithm that decides on all the color changes they don't want to spend time doing. It takes less time than recoloring a set of shinies by hand, is completely reusable for games on the same engine, and a starting point when they make a new engine.I'm sorry but what? Do you have any experience doing this sort of thing or are you just talking out of your ass? Because I can guarantee that if you know what you're doing, making a shiny version of a texture for a model takes less than a minute to make.
Let's suppose they have every different color of a model on a different layer in a .psd file. If you look at existing textures, you can see that they have very basic shading, so those are probably on a separate layer as well. Now all you have to do is move around the hue slider a bit for each layer until you get your resulting shiny texture.
Pokemon with similar colors having similar shiny colors is an artifact of the old games and their sprite-based images. Since they all used palettes, shinies were made by just making the sprite use a different palette, which is why so many old pokemon have a bright pink or green shiny. Once they moved to standalone textures like in XY, they were able to color shinies however they wanted, which is why there's so few shinies (if any) that are either bright pink, green, or look almost identical to their base colors (like gengar and garchomp).
Since those colors were the same before XY that doesn't help your point.