John, heat can disguise excessive gluten formation.
Gluten contributors:
1. Kneading
2. Resting
3. Extended (but not too extended) Fermentation
4. Late balling/Re-balling
5. Older flour (to a point)
6. Salt
7. Acid
8. Excess water
9. Rough handling during the form
10. Long Bakes (for Caputo)
Kneading/Resting/Extended FermentationWindowpaning should play no role in great pizzamaking. The only area where windowpaning works is with emergency doughs, and those, as the name reveals, should only be used in emergencies because of the sacrifice in flavor and digestibility. This is especially true for commercial Neapolitan pizza, where space sufficient for extended fermentation isn't optional (like NY), but mandatory. A Neapolitan pizzeria serving people a same day crust is destined to fail. Water + flour + time = gluten. It doesn't matter if it's an autolyse, a rest, or the time spent in fermentation. Any dough fermentated longer than overnight should be kneaded minimally. Lower protein flours such as Caputo tend to be a little more forgiving to overkneading, but you still want to be careful and avoid anything close to windowpaning. I use a cottage cheese appearance as an indicator for kneading 2-3 day fermented NY doughs. Since Neapolitan is generally less fermentation time than that, I'd recommend shooting for somewhere in between cottage cheese and smooth. I would also, at least once, try a cottage cheese appearance and see where it gets you.
Balling/Re-ballingEven with plenty of rest (6 or more hours) after balling, I still think post-bulk ferment balling might contribute to toughness (at typical elevations

). Maybe. If you've tried everything else and are still getting leatheriness post or pre-cooling, try a pre-ferment ball. Re-balling is, imo, out of the question. I know some members re-ball to avoid too much dough spread, and, while I think avoiding dough ball touching is important, re-balling is not the answer. Tender, minimally kneaded dough
should spread a bit and you should allow for this by placing fewer dough balls in each container and staggering them diagonally or using individual containers.
Older FlourThe age of the Caputo flour in your cupboard is always going to be a question mark. Caputo seems to be somewhat tight lipped about flour manufacturing, so I'm not certain as to how long they age the flour in-house. Since it's unbromated and they have local pizzerias that need to work with it immediately after purchasing, I'm sure they age it a bit. Since the Caputo we get in the states is coming from Italy and purchased from specialty stores with potentially poor turnover, that could translate into older flour in our American cupboards, or, some of us make get lucky and latch on to a more direct/faster source. There's also a very likely possibility that you might purchase a fresh bag on one occasion and an old bag on another. Not only should you, like all professional bakers, approach each shipment with the expectation of slightly different results, you need to be aware that if you go through a bag of Caputo slowly (longer than 6 months), there's a potential for the end of the bag to form slightly more glutenous doughs than the beginning.
Now, as a flour ages, it doesn't keep increasing gluten forming potential indefinitely. There is a point where it's gluten potential will reach it's peak and any further aging will have no impact. Assuming Caputo ages their flour in-house, this should lessen the disparity between flour that's obtained quickly from the manufacturer and flour that's sat around. Also, the gluten potential differences I'm talking about here should be pretty minimal. If the age of the flour is contributing in some way to leatheriness, it's only part of the problem.
SaltSalt is pretty straightforward. Exceeding 3% will give you both gluten and fermentation issues, but I don't see any of the bakers on this board doing that, at least, not intentionally. I think the most important aspect of salt is to stick to the same amount and measure it carefully.
AcidAcid in non-sourdoughs is also pretty straightforward. In longer ferments, you will find some CO2 dissolving into carbonic acid causing some gluten strengthening, but you'll also find some weakening with protease activity. I don't think one really needs to focus on pH when dealing with non sourdough reasonably fermented (less than 2 days) Neapolitan doughs. The one thing that I would do regarding pH, is, like salt, pick a fermentation routine (time and temp) and try to stick to it.
Acid in sourdoughs... forget about it

. I can completely understand why pizzerias like Da Michele and Keste avoid sourdoughs. It brings an unbelievable layer of complexity to the equation. If you are using a starter and experiencing leathery crusts, I'd try switching to an all fresh yeast formula, seeing if that resolves the leatheriness, and, if it does, start analyzing your sourdough approach closer. A useful tool in that battle might be a pH meter like the one Norma has.
WaterI don't see a lot of documentation on this, but I have found personally, that if you go too much above a flour's absorption value, the crust can get tough. At least at lower elevations (I don't think Bill and Chau have ever produced tough crusts and they regularly work with higher hydrations). For the rest of us, though, I don't think we should be exceeding 60% with Caputo, with 58% being the sweet spot for the best oven spring while still achieving good tenderness.
Rough FormingThe slap method, although fun to do and watch, might be a bit counterproductive when it comes to tenderness. It's great for developing gluten in the undercrust and giving it a bit more tooth, but... even when done correctly, it still stresses the rim more than a gentle knuckle stretch. Although neither Bianco nor Lahey make pure Neapolitan pizzas, they do put out amazing and relatively tender products and both are renowned for doing incredibly gentle forms. I find that if I slap the center of my finger pressed dough, the gluten will tighten and, when I go to knuckle stretch it, the center will have far less propensity to thin out. But that's with the dough on the bench and I'm making sure to slap only the center of the dough. If tenderness is important to you, I'd avoid the jerking of the rim in the traditional Neapolitan slap technique.
Longer BakesI know there are some advanced pizza making alchemists on this forum that are pretty proud of their longer Caputo bakes, but, for the rest of us, I think it's a good idea to keep Caputo dough bakes to under 90 seconds, as Caputo doughs have a very strong propensity to produce tough crusts when baked longer.
Summing up, here's my recommendations (try one at time)
Enough kneading to produce a slightly cottage cheese-y appearance
Pre-ferment balling with staggered container placement
Flour age awareness
If sourdough, experiment with non sourdoughs to rule out other factors
58% hydration (or possibly even 56% if you're doing less than a minute bakes)
Gentle forming
Sub 90 second bakes for Caputo
Lastly, if all else fails and you want to guarantee tenderness, I would play around with lower protein flours. I know Craig has achieved pretty amazing results with KAAP, and although KAAP has a higher protein than regular AP, it's lower than Caputo. Indian bakers making naan at very similar temps to Neapolitan achieve very tender crumbs and great oven spring with lower protein flour. I would suggest avoiding malt, though. A 50/50 pizza 00/pasta 00 might be a good jumping off point.