Its tough to relate the endocrine glands to these types of phenomena. Even though the hormones and chemicals produced by the glands have a big effect on all the mental and physical systems, the endocrine system still operates on the gross (physical) level.
The chakras are involved with energies and functions that are more subtle. It seems like you’re on the right track towards identifying your mystery-rainbow object though, the bindu is thought to reside within the centre of the Kutastha. The chakra that is nearest to the Thalamus of that picture is the Ajna centre, which is known as the seat of the soul (which by extension is also the “over soul”).
Here’s what a kriya scholar wrote about this object:
“The form of kutastha is threefold: 1. An outer golden disk 2. An inner blue disk, and 3. A white star in the centre. The star was often called Bindu by Lahiri Mahasaya. It is the manifestation of the absolute within the field of consciousness.”
This form is not set in stone however. Different people at different stages can have different visions of this thing.