Aloha Skipper,
Master Lin isn't targeting the Chakras in that meditation. If asked the question, he'd probably smile and say "If you want to stop and focus there, go ahead," The mediation is working at many different levels, areas, and things. The chakras doend up benefiting.
There are versions of the microcosmic orbit (Small Universe) meditation that cover over one hundred locations, have specific breathing and colors at each place, etc. Chunyi uses this version because he founds it keeps things simple and yields the most benefits to the practitioner. Consider letting go of fitting things into a chakra paradigm and just be with the meditation as led.
Some things to consider:
There may be times that you find yourself "stopped" at a certain area - whether it's a spot on the rotation, or not. For example you may find your self pausing at the base of the head area and not wanting to move just yet - honor that, allow yourself to spend however many breaths you need there and move on when it releases. You may find yourself stopping at an area between the shoulder blades - honor that, and move on when it releases.
This is not to say you go around I felt like stopping here, or here, or here, rather there (may) be times that some spot holds you to it for more than a breath, or holds you in a spot that's not a stopping point, be with it and then continue with the Small universe locations of the meditation.
Much Love, Shawn
