There are no more actual fuses, but JTAG access can be limited or completely disabled on most (or possibly all) modern ARM chips by setting a value in the non-volatile (flash or EEPROM) memory. Even the IC manufacturer (Freescale, ST, etc.) can be locked out completely.
Most ICs can be completely erased to remove the limitations on access, but this usually requires a 'mass erase', where the entire non-volatile memory is erased (taking any codes, passwords, and encryption keys with it).
source: I am an embedded software engineer who works with these settings in bootloaders and application software.
I would not be surprised at all that Apple's internal 'backdoor' (if you can call it that) is just resetting the security enclave, essentially erasing everything on the NAND. That'd be fine for refurb/manufacturing, desirable even as that guarantees that full system wipes happen before a refurb goes to a new customer.