Hi Gabe,
I assume by "bindu" you mean the bindu chakra on the top back of the head rather than bindu above the crown chakra?
Yes, there are definite advantages to using the third eye as the end point of Spinal Breathing. The third eye is the ajna chakra in Sanskrit which means "control". It is called that because it gives a great deal of control and stability over the inner energy flows in the body. If things become unstable higher up, we can use the ajna to stabilize the awakening and produce a smoother journey.
The second reason that I would not recommend using the bindu chakra is because it is too close to the crown and too closely related to the crown energy wise. the crown chakra is a very unstable chakra and activating it too early on in the sadhana can bring about a lot of problems which are not easily remedied.
So my advice would be to stick with root to third eye for Spinal Breathing.
Regarding your second question- if you are able to feel the flow of prana in your body and that flow is not happening in your spine, then follow the flow of energy. The end point should still be the ajna chakra at the brow though. If the flow of prana is going to the crown or bindu, then bring your attention to the brow instead. As the body purifies and the shushumna nadi broadens it also comes forward, leaving the spine and coming more towards the centre of the body which is why you are experiencing a flow separate from the spine.
Christi