Waffle Dough – Effects of Over-Resting Dough with Yeast

1. the amount of flour is likely the culprit. Flour is very sensitive to moisture and can change volume a surprising amount so that the two cups may not be two cups. Also make sure you are not scooping the flour out with your measuring cup, but filling it with another implement before leveling off the top with a straight edge.

2. As you are after a not-quite-bread-like consistency, even though you are using high-gluten flour (in the bread flour called for) you don't want a full bread-like texture

3. Letting the yeast rise

4. Many sweet breads do something similar. Cinnamon buns for example. It again affects the crumb and texture of the final product. It also slows down the yeast as it notes in the recipe when you refrigerate for just a little bit. The rise the next morning should give you nice small bubbles.

In addition to allowing fermentation to begin before the addition of fermentation inhibiting other ingredients, as @J.A.I.L. said in his answer, according to Bread Secrets, after explaining the benefits to flavor of a long, slow fermentation:

A quick, warm fermentation will allow time for the yeast to produce enough carbon dioxide to raise the dough, but not enough time for the enzymes to work or for the development of the other flavour compounds. If we ferment our dough for too long, however, the gluten becomes too weak to hold the shape of the loaf. So artisan bakers generally use a preferment (pre-ferment, not prefer-ment!) as part of their dough. This allows the bread to gain flavour from the longer fermentation, but still maintain a strong gluten network for a good rise.