- Essentially, Cakras, like anything else, may functional less optimally, and tools like Sapien’s audios, meditation, breathing etc., are to optimize these centers. So yes, this can be viewed as correcting their alignment. Can this be called “crooked” chakras, I don’t know!
- Chakras can be sensed physically in the sense of a Kshetra. Every chakra has a specific kshetra – a contact point through which it can be accessed – and according to some folks, this may is related to a specific endocrine gland. This Kshetra can be a physical (an organ or physical body location) or internal (a specific space within the body representing the energy of the chakra consciousness).
As Chakras represent the evolution of consciousness from one to many, and hence the creation metaphysics espoused by chakra-based systems, one can work with higher centers directly, if and only if - the level of consciousness permits it. For example, generally, Root Chakra based practices are used to awaken the Kundalini, but more advanced Yogis may rely only on the Ajna (Third-eye) center which is directly related to the root (chakras are symmetric that way) to awaken the energies of the root. In our school of Tantra, Kundalini is awakened in the Solar Plexus chakra and not the root chakra for certain reasons.
Also, Chakras were never practice on their own, but a part of larger systems, one of the tools in the toolkit. Similar to Meridians and Dantien concepts used in other energy systems. It is just that chakras seem to have become more popular in the West through the theosophists (not nadis for some reason).