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I don't recall having to reset OS X to be the default OS to boot when I updated my own MacBook to Sierra. Overall, I'd say that inadequate unpartitioned space following the OS X boot partition is the more likely explanation. Backing up important data from the disk, and especially from the partition(s) you modify, is important when modifying partitions in this way, or when installing an OS. Alternatively, you could shrink the partition that follows the OS X partition but moving the start point of a partition is almost always riskier and more time-consuming than moving the end point. If Apple's Disk Utility won't let you adjust the OS X partition size, you might try doing the same thing using GParted in Kali. Basically, Apple's installers want to see 128 MiB or more of unpartitioned space after the partition to which the OS is being installed. When installing Kali, you didn't include adequate unpartitioned space between partitions - This is the issue that the page to which you pointed addresses.(You'd basically treat it as if you were recovering from a boot coup.)

After installing Sierra, you'd need to re-install rEFInd, or at least reset the existing rEFInd as the default boot option.

To work around this problem, you could use the Startup Disk item in System Preferences to set OS X to boot directly, thus bypassing rEFInd. The Sierra installer dislikes rEFInd - It could be that the Sierra installer sees that a non-Apple tool is in charge of the boot process, and is therefore refusing to run.I can imagine a couple of possible causes of this problem, each of which would have a different solution: