The Secure Element is part of the NFC chip described in [[1]] and used to store the commands, signatures and cryptographic keys used in ApplePay transactions.
The programming interface is spread across the following binaries: /lib/exec/seld /usr/lib/libnfshared.dylib
Unlike the PN548 element - the commands for the secure element appear to be embedded in the seld daemon.
Communication to the secure element is performed through XPC calls to seld.