Hmm... The dough I use recquires a few folds over 40 minutes then refrigeration overnight-4 days. And then I take it out and rise it again.

I do go back and forth about handling the dough too much and getting the weights just right or not. For pizza I try not to get too obsessed.

It does rise in the fridge and I can tell if I ran over 40 minutes or the kitchen is hot. I find plastic dough buckets the easiest to use. But if space is tight I use 1 gallon ziplock bags with a little olive oil.

Weighing is the only way I've found. I don't mind if the balls are not uniform since I'm not selling them. :) If you--without a lot of handling--make a kind of flat topped rectangle or square out of your original heap of dough, it's easier to cut by sight and be in the neighborhood. Then lift a section, weigh in your hand, weigh on the scale, and wrap it up. Do the next. If you make pizza regularly and constantly check the weights, paying close attention, you'll train yourself to cut more accurately. I have been known to trim or add and it doesn't really hurt anything, but I don't pull balls with my whole wheat. That's probably the answer. Weigh your divisions first, then pull your balls after adjusting. Or you can just leave them uneven and try to do better next time. :)

What kind of yeast are you using? For a long rise like that, active dry yeast should be fine. If you're using instant, it may be rising faster than its cooling and growing a lot before the chill retards it. (That's speculation--I haven't done that.)

You can also put your dough in the coldest part of the fridge (crisper? meat drawer?), or even start it in a pan of ice for a quick cool down.

My dough also rises in the fridge--it all does or it would be dead. It doesn't over rise, however. I learned a trick online which I think helps contain it. Instead of plastic wrap, I use zipper bags (a small to medium will fit in a thin sandwich bag). Spray or brush the inside of the bag with a shot of oil first. Then I put my bags of balls into a large zipper bag. After a few days, the yeast burps do start escaping the little bags into the big one, but everything is well contained. If the dough has risen a lot in the fridge, I also am more careful on shaping (gentle pulls with gravity rather than a knucklefest), which helps it not to de-gas.

I have found that the brand of flour I use makes a big difference in how it handles. King Arthur works by far the best. Pillsbury, which I had to buy once when the store didn't have KA was much more sticky and very hard to work with.

I use several different kinds of flour, King Arthur, Pillsburys, Gold medal, supermarket brand and my favorite Montana Wheat....but for pizza dough, I see no difference....and if you ae seeing a "big difference" there is something else going on there> I will bet I can make 5 batches of dough, same recipe, different brands of flour and by touch you can't tell any difference.

Whether or not you can over handle depends on the dough. The home milled whole wheat dough I make won't stand up to a lot of handling because the bran cuts the gluten. Gentle shaping without pulling means that it will continue to rise. Pulling will make it into flatbread. I've seen recipes for white flour pizza that also say not to handle a lot after the knead, though I don't know why, for sure. Probably to keep it from getting tough.

King Arthur recommends kneading whole wheat bread for 7 or 8 minutes. Other sites recommend longer kneading. Whole wheat flour contains a smaller percentage of gluten than white, for a really good rise on a whole wheat bread add about 2 Tablespoons of gluten flour per loaf....and knead long and hard!
Kneading doesn't make bread tough...unless you are constantly adding flour. and get your dough too dense.
Just wondering where you heard that over handling of whole wheat flour makes a flat loaf, and where you found a recipe for pizza crust that says not to handle a lot after the knead?

I said pizza and it's my experience, with my very good pizza dough--which does get kneaded before it's portioned--that the more it's handled after it rises the more it de-gases permanently. You can actually see where the gluten strands are cut. It's a well known phenomenon. The dough will still bake, but it'll be flat. This is with home milled flour, however. I don't know if the commercial whole wheat flour does something to the bran to lessen the effect. Since whole wheat needs to soak, the gluten develops over time rather than by a lot of manipulation.

Overhandling bread dough (white flour) making the bread tough is a well discussed issue. I was taught not to do it, and any number of books and recipes say so. If you have research that shows otherwise, please share. Lots of received information is wrong, such as that soaking beans improves the cook and/or lessens the effect of the fiber on digestive gasses.

Well....this is a video I copy when I make a white bread.....and a similar method works with a pizza dough. Notice the very rough handling after the rise.
However I didn't know you were looking for a tender biscuit like pizza crust, most like a dough with some tooth to it.
If you pound the gas out of your dough....let it sit for1 5 or 20 minutes and the yeast will continue to work, unled you have somehow killed the yeast by heating or allowing it to proof for more than a week to the point that it has used up all the food in the dough and the yeast has died.....which would make a very sour dough.
I don't really know of any kneading that you could do to your dough that a short sit in a warm place wouldn't fix. Handling risen dough where the gluten has been developed can make the dough resistant to rolling, it will snap back at you when you try to spread it out....let it sit for 20 minutes and it will relax. Pound out the air and it will puff up again.
I have been making bread a couple times a week for almost 50 years....never experiences what you describe.
https://www.youtube.com/watch?v=9iH3hjDUhWw

It's not about killing the yeast. With the whole wheat, it's about cutting the gluten. It doesn't matter what the yeast does when the gluten strands are broken. The overhandling issue is received knowledge, not experience, as I said, and I was responding to the questions asked. I'll leave it to you to argue with all the recipes that say not to do it.

I didn't say that all dough is like this, but you can't say that all dough is like yours either.