Conscious brain activity always struck me as the primary meaning of "thought". The idea of conflating "thought" with unconscious brain activity just seems to devalue the word itself rather than bring some utility or added understanding to the table.
Personally, I don't think of breathing as a thought at all, or my heart beating, even though it's evidently controlled by the brain, evidently also the source of thoughts. I only really ever have evidence of thoughts as distinct from other brain functions because I experience them consciously.