Baking – Flourless cookies form “skin” that seals in moisture

I'll try to be specific without getting into too much detail here:

1. The chewiness (AKA elasticity) - of dough is due to the formation of gluten. This is affected by:

   • The amount of flour used (gluten is the result of water and various proteins in flour, specifically glutenin and gliadin);
   • Type of flour used (high-gluten flour such as bread flour gives means a chewier result);
   • Fat content (fat insulates the proteins from the water, slowing gluten formation);
   • Sugar content (in order for gluten to form, it must be dissolved; a high sugar content saturates the water and prevents dissolution of the proteins);
   • Baking time (up to a certain point, until all of the available proteins have been used up).
     
     

2. The crust (I assume this is what you're referring to by "softness") - is primarily the result of the Maillard reaction, which requires an amino acid and a sugar as well as heat. The longer and more quickly the reaction carries on, the crispier and browner the crust will be. The factors are:

   • Baking temperature (higher = crispier);
   • Baking time (longer = crispier);
   • Moisture (less = crispier). This has an effect because the evaporation temperature of water (100° C / 212° F) is lower than that required for the Maillard reaction (154° C / 310° F), so the reaction can only take place once all water has evaporated or been converted to gluten.
   • Acidity (pH) also inhibits the Maillard reaction but this is not normally a concern in bread.
     
     

3. Finally, the moistness of the bread is essentially a combination of the first two:

   • Higher fat content means less gluten is formed and more of the moisture is preserved, as long as it doesn't evaporate. The fat itself also adds a certain amount of moisture as far as mouth-feel is concerned.

   • Higher sugar content also preserves more of the moisture and using a wetter sugar (i.e. brown or muscovado) provides some moisture of its own - although the latter can easily evaporate with over-baking.

   • Longer baking times cause more of the water to evaporate, which reduces the final level of moisture in the finished bread.

   • Higher baking temperatures also cause more water to evaporate. However, it's usually a trade-off between higher temperatures or longer baking. A good recipe tends to be optimized to provide a slightly crispy crust without over-developing gluten or drying out the bread.

If your bread (or similar baked product) ended up too dry, it's probably because you over-baked it or baked at too high a temperature. If it came out too chewy (glutinous), you might have used too strong a flour or not enough fat/sugar.

Peanut butters that are not "all natural" include cheaper oils along with sugar and emulsifiers to keep the mixture from separating and to make it lighter and smoother.

That lack of emulsifiers could make a huge difference but it depends a lot on the recipe.

In a normal cookie dough fat is creamed with sugar and eggs are beaten in one at a time which adds a ton of emulsification power from the lecithin in the yolks.

Additionally- the fat will bind with the flour and be baked into the cookies. Like Jefromi- I have not had any problem with the fat from natural peanut butter separating out after baking.

If you made a cookie dough and either left out the yolks or didn't beat it well enough to properly emulsify- and then let the batter sit out for a while before baking I would fully expect the peanut oil to separate.