One example is the application of decals. Many folks use flat/matt paint if the final finish on the model should be matt. But decals do not work well over flat paint. So you need to apply a gloss clearcoat, at least in the areas where decals go. Then, to get the final flat finish you need to spray with a flat/matt clearcoat.
Sometimes you cannot get the color you need in the appropriate sheen. So you can change the sheen by using the appropriate clearcoat. Getting a really good shine with gloss paints can be difficult- gloss clearcoat can change a sort-of-gloss to a really glossy sheen,
I have read also that applying a gloss clearcoat helps you when wathering your model. Do you know if you will get the same results with a flat/matt clear coat?