Generally with baking you mix all the wet ingredients, then all the dry, then incorporate the latter into the former. This prevents clumping and helps make sure everything is mixed uniformly.
In some recipes, adding the eggs (often un par un, or one by one) also contributes (via the yolk's supply of lecithin) to emulsifying e.g. butter and milk together.
The best way to find out, of course, is to experiment. Next time you're making these cookies, make a double batch. Do one according to the recipe, and the other your way. Honestly with cookies I doubt you'll see much difference; they're basically foolproof (I have, when in a hurry, made chocolate chip cookies by dumping everything in the mixer, whacking it about with the paddle attachment, and then folding in the actual chips. Worked fine, basically). When it comes to baking things that are more finicky--cakes etc--I would follow the recipe directions.
Preheat while doing other things. That's not a step that should take any effective time.
Don't measure so obsessively. Unless these need to be immaculate cookies, just accept a little variety. Scoop roughly with a spoon, or just your hands, and form into balls with your hands if necessary. If you desperately want precision, you could use a cookie dough scoop. But 56±3g sounds kind of over the top to me. Given that you said this is the main time sink, I'd suggest loosening up a bit.
Are you filling your cookie sheets fully? Do they fill your oven? Following a recipe's instructions to the letter, baking only 9 per sheet, is obviously the wrong thing to do if your cookies or baking sheets aren't the same sizes as those in the recipe. Note also that if you have many cookies per sheet, you can often fit more by tiling in triangles instead of squares.
And finally, reconsider your recipe. I'm sure this one is great, but keep in mind that most standard chocolate chip cookie recipes bake at 350F or 375F, and times more in the 8-12 minute range. If your recipe gives you exactly the cookies you want, and others don't, then stick with it, but if you're unnecessarily sticking to a recipe, try something else.
Edit: one more thought! Chilling the dough is probably important to your recipe, but you could measure/scoop while it's warmer and easier to work with, then chill in balls, and do the final forming once chilled.
And another, having seen your comment: given that you increased the baking time upon filling up the oven more, and are using insulated pans, you might actually want to increase the temperature to 350-375F and see if you can get back down to the 15-18 minute baking time. They may end up closer to the originally-intended consistency!
Best Answer
The steam and other hot gasses that were puffing the cookies up either escapes or condenses. Without heat to create more steam, the cookies deflate.
You get exactly the same effect with bread, quiches, and other baked goods. You can hear bread start to make a crackling sound almost as soon as it comes out of the oven, and the sound continues for some minutes until the bread has cooled a bit. Quiches are always quite puffy looking when they're in the oven, but they start to shrink a bit as they cool.
If you want your cookies to shrink less, you might try cooking them at a slightly higher temperature, or cooking them a bit longer, or perhaps not chilling them so much prior to baking. Bumping up the amount of egg white in the cookie may help, too. The idea is to get the structure of the cookie to set a bit more by the time you remove the cookies from the oven. That will, of course, cause the cookies to be less chewy and more crunchy.