I can't edit my post above any longer, so hopefully others will see this since I'm putting my updates in replies to myself.
First, I want to correct myself. I originally said above that both the mobile wallet payments and the directly entered credit card payments were in both payouts. It turns out I was wrong. After going back through every single order in all of our new smaller payouts, it turns out that both payouts DO have mobile wallet payments in them, but only the larger payouts have the credit card payments. The smaller payouts don't have any direct credit card payments.
Second, I want to add a couple of other things I found.
The differences I noticed in regards to the "transaction message" field and the format of the authorization key exist for both the payment authorization and the payment capture on the order. We capture payment only after the order has been fulfilled, so for us there is usually a day or three between the order getting placed and being shipped. This can work as a little heads up about which way a given order may wind up going. One interesting note here is that for the orders in the larger payout, the authorization key is the same in both the payment authorization and the payment capture. But in the smaller payout, these keys are different within the same order.
Another thing I noticed was, when looking at the receiptjson field in the API, all of the orders that wind up in the smaller payout have links and references to Paypal. But the weird thing is that these were NOT paid via Paypal. They're all Shop Pay and Apple Pay. Our orders that are actually paid via Paypal don't even show up in Shopify's payouts and transactions, which makes sense. I just don't understand why the Shop/Apple Pay orders in the smaller payout have the Paypal references and the ones showing up in the larger payout do not.
Finally, we have also run into a couple of orders that were edited to add items after they were initially placed, but before payment was captured. Even if the customer used the same credit card before and after the edit, but switched to entering the credit card info directly instead of using Shop Pay or Apple Pay, the payout for that order was actually split between the two payouts! That one is particularly annoying because it means that the money for a single order gets split across multiple days. We have the same thing happen if an item gets added to an order and the first payment was with Paypal but the second is via credit card or mobile wallet. But in that case, with the payouts coming from different sources (Paypal and Shopify Payments) that one made more sense, at least.
I'm not sure how much these observances translate to other stores, but they're just things we've noticed in ours. I'll continue to follow up if I find anything else.
