One fun fact about the instructions, I recently learned from a Lego designer that the reason they use many different colours on the inside of most models is to make it easier to see what's going on while you're building. That explanation never occurred to me, but maybe it's obvious.
I noticed this after buying a crapton of legos on craigslist for, um, my new kid! I do have a new kid, but anyway, the colors vary far too much now.
Charitably, the colors probably subtly act like antialising does in rasterization, so it might make a blocky model seem more organic. But I think the business of selling more sets is also a sneaky reason.
Nowadays there are so many custom pieces and people don’t really rebuild much anyway, so they don’t even need to discourage what you describe using colours.
One thing they seem to have lost over the years is the flexibility of the kits: I remember many kits having instructions for several alternate models, encouraging you much more to take things apart again after building. Newer kits are mostly a single model and that limits the fun that you end up having with them. The invitation to tinker seems gone.