Why is it secure to reuse key and nonce in ChaCha20-Poly1305 AEAD construction?
Actually, by your own criterion, the same nonce is routinely used much more than twice, because each call to the ChaCha20 core function reuses the same key and nonce, except with a different counter value.

Here's the problem that's tripping you up: the prohibition on using the same key/nonce pair to encrypt more than one message applies to the construction's callers, not the construction's internals. The implied tension you're reading between the external requirement and the internal details just isn't real.

But, internally, the fact that each call to the core function within an invidual encryption operation uses a different counter value is relevant here.