The MMCSD_enableBootPartition sends the CMD6 to configure the EXTCSD register with the following arg

uint8_t bootPartition = ((bootAck << 6U) | (partitionNum << 3) | partitionNum);
uint8_t bootBusWidth = 0x02;
uint32_t arg = (uint32_t)((bootPartition << 8) | (0xB3 << 16) | (0x03 << 24)); 

This means, it configures the EXTCSD register as follows:

• Enable the Boot Acknowledgement flag.
• Change the boot partition, which ROM uses to boot from in eMMC alternate mode, to the passed partition number.
• Enable access to the passed partition number.

The first two configurations are completely independent of the last one. There can be a case where one wants to enable access to, let's say, BOOT1 partition but not wants to change the boot partition from which the ROM boots the SBL Stage1.