Actually, we're pretty sure that the same principle that makes a soufflé rise was happening in our bread pudding. In a soufflé, whipped egg whites are folded into a egg yolk base. The air bubbles in the egg whites expand in the heat of the oven, causing the whole network of egg proteins to lift ("rise") the dish.
When making a cream and egg custard like flan or crème bruleé, the goal is usually to minimize the air bubbles for a creamier and more uniform texture. Also, the eggs are normally so diluted by the cream that the protein network that forms is much more delicate. Even if there are air pockets, they are unable to lift the fragile network.
We think two things were going on in our bread pudding. For one, we whipped together the cream and eggs for several minutes to get the uniform consistency specified in the recipe. Although the recipe didn't talk about incorporating air, that's most certainly what we were doing.
Secondly, there was a higher proportion of eggs to cream in this recipe than is normal for custards - it was roughly one part egg to two parts cream (the ratio is normally more like 1:4).
This meant that the protein structure, while still relatively weak, was stronger than normal. This probably helped to retain the air bubbles in the mix even after the dish stood for several hours before baking and also helped it puff up in the oven.
That's our theory! What do you think?