Does allowing apples to brown before long cooking affect the final flavour?
Browning is oxidation. Oxidation has a distasteful affect to the flavor of many fruit where the star flavor profiles are acidic in nature. In apples, the two acids are malic acid and tartaric acid. Oxidation in combination with these two acids gives apples an artificial candy flavor.

Now I realize this isn't an apple example, but it is a good way to really taste what oxidation can do to fruit and fruit flavors. If you can, find some good strawberry wine (yes it does exist), and then try some cheap strawberry wine. Cheap strawberry wine tastes like strawberry candy, while good strawberry wine tastes like the refined version of the fruit. The difference is the amount of care given to avoid oxidation of the fruit and wine at all stages of the process. Strawberry wine is so easily oxidized that you need to fill chambers with nitrogen gas to keep air away from it. Cheap winemakers don't go to the trouble or additional cost since they are selling at a thinner margin.