You are correct that metabolism generates heat which needs to be lost in order to maintain a certain temperature. The body is capable of keeping temperature withing a narrow range even as metabolism and energy expenditure increases, however. If metabolic rate increases, the hypothalamus will initiate increased sweating to compensate. When water on the skin evaporates, it cools the body.
This may seem to contrast with the idea that thyroid hormone increases metabolism *and* also increases body temperature. There is evidence that suggests that the increase in body temperature associated with thyroid hormone is not caused by the increased thermogenesis (heat generation) but rather by some other mechanism.
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