They've published several whitepapers and technical documentation on how the secure enclave works and it's been poked at by security researchers for years.
If it's not open source (with open hardware), you cannot trust it. Whitepapers are great, but who knows what's actually implemented.
Exclaves are much newer and not well documented
They have been. Through years of use, independent auditing, industry and government certification processes, and their Apple Security Research program.
This is a brand new product. Basically nothing what you wrote applies to it. Also, I cannot find any public independent audit result for this specific product. Heck, I couldn't find even a single one about any Apple products, what I found all of them said that they're not verification at all, and of course Apple never published anything related to these.
Apple can’t prove a negative. You have to prove they’re lying.
You don't have to prove anything. You need to asses your risk profile and decide if you want to expose yourself to Apple or not.
You can. They do all the time in math and programming.