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Why does holding ice cream mix overnight prior to churning improve the flavor of ice cream when it is finally made?
This is true, empirically in my experience, even for simple Philadelphia style ice creams with very simple flavorings such as vanilla and coffee.
Main reason that comes to mind is, for the same reason compound butter's flavour improves over a couple of days: infusion.
Fat can be infused with flavour, and holds flavour incredibly well, but it needs a little time (viscosity of fat vs water). Otherwise the fat in Serrano Ham would taste just like it would on day one.
By holding your mix/custard overnight you are allowing the coffee or vanilla flavours get infused into the mix. You can somewhat accelerate this by letting the vanilla sit in hot ice-cream mix for 1hr as suggested by many pastry chefs (e.g. Simple French Desserts, Jill O'Conner). I suspect the acceleration is due to the lower viscosity of fat at higher temperatures. The taste does follow the physics here were the higher the viscosity the longer infusion (read equilibrium) takes. Serrano ham: two years. Hot deep fryer oil: seconds.
By the way, when it comes to ice-cream, they also recommend aging your mix/custard for up to 48 hours. It may be worth the experiment to sous-vide your ice-cream batter/mix at say 55C for a couple of hours and compare taste with the over-night version.
Although mouthfeel may play a role in this case, the 'flavour improves over time' effect is present even when crystallization is not happening.
Ice Cream Science - Aging the mix was the best reference I could find, though I haven't had a chance to look at Modernist Cuisine and Food and Cooking yet. Basically, it improves mouthfeel, allows more air to be retained (this could be good or bad depending on your opinion of overflow), and helps slow melting. All of the cited reasons have more to do with mouthfeel and texture, rather than taste though.
(i) Absorption of Emulsifiers
Two important changes take place during the aging process. First, the emulsifiers (lecithin from the egg yolks) absorb to the surface of the fat droplets, creating a weaker membrane that is more susceptible to partial coalescence.
When the mix is frozen in the ice cream machine, it undergoes partial coalescence, during which clumps of the fat globules form and build an internal fat network (Marshall et. al, 2003). These fat globule clumps are responsible for stabilsing the air cells and creating a semi-continuous network of fat throughout the product resulting in a smooth texture and resistance to meltdown (Tharp et al, 1998).
(ii) Crystallisation of fat
Second, the fat inside the droplets begins to crystallise. Nearly complete crystallisation is needed to promote coalescence of fat globules during freezing (Marshall et al., 2003). Cooling mix to 0-2°C increase the rate of crystallisation. Barfod et al., 1991, showed that crystallisation of fat in a mix containing 10% fat requires at least 4 hours.
If you do not sufficiently age your mix, your ice cream can suffer from defects similar to those found in mixes with no added emulsifiers: less retention of shape and relatively fast meltdown (Marshall et al., 2003). It will also be difficult to stabilise air bubbles during the whipping stage, resulting in a hard chewy texture.
Mando's answer plays on popular conceptions of flavors infusing or "melding" over time, but in most cases this isn't a possibility. You may get some added infusion if a vanilla pod or herbs are left in the mix as it ages. This may or may not be good (just as tea that brews for a very long may not be good). And in cases where the flavoring ingredients have been removed, there is no process that directly effects flavor.
But there are many processes that will effect texture, and these will have a strong indirect effect on our flavor perceptions. The most important is Matthew's #2 answer: the fat molecules need to crystalize in order to become whipable. His #1 answer is also significant. Any gel-forming compounds, like egg custard, gelatin, or other stabilizers, need time to form their molecular networks. And if there are other stabilizing ingredients, like gums, they can take hours to hydrate fully. It's not just industry that uses these ingredients; you'll find that most of the best pastry chefs use them as well. They improve the texture of any ice cream when used properly.
