I would recommend splitting the vegetables: some from the start for taste and some later for show. The first ones are discarded when sieving/reducing the sauce. The others can be coloured by roasting or glazing in water/butter. You can also shape them the way you want and preserve that shape. This will achieve your twin objective of taste and looks.
I roast the root vegetables, then add for the last 30 minutes. I find boiled vegetables uninteresting. Roasted vegetables bring flavor and great texture.
Trying to time it just right to the meat's doneness is almost impossible. You never know how long the vegetables will take in the stew.