These sources are understandably couched in their language, but wikipedia is more certain:
All the metabolic wastes are excreted in a form of water solutes through the excretory organs (nephridia, Malpighian tubules, kidneys), with the exception of CO2, which is excreted together with the water vapor throughout the lungs. The elimination of these compounds enables the chemical homeostasis of the organism.
They go on to mention some other gases produced by other organisms such as denitrifying bacteria, but these are not related to the human respiratory system.
On the other hand, chemical analysis of breath apparently reveals a large number of volatile organic compounds (among other constituents), presumably related to metabolic activity:
In exhaled breath, more than 3500 different components have been found and the list is continually growing. The complex matrix of exhaled breath component is termed as molecular breath signature 2. The actual breath is a bulk matrix and contains mixtures of nitrogen, oxygen, carbon dioxide, inert gases, water vapor and a contain thousands of trace volatile organic compounds (VOCs) and inorganic molecules such as NO, NH3 or CO.
Moreover, a different distribution of such trace compounds appears to be diagnostic for some diseases, indicating that $CO_2$ is not the only waste business in town:
Human breath contains a myriad of biomarkers resulting from the blood by passive diffusion across the pulmonary alveolar membrane 2. Breath testing offers a novel approach to the disease diagnosis, evaluation of various common disorders, and assessment of exposure to VOCs .
I think that a good way of reading your quotes is as follows:
"Human respiratory waste gases include a lot of $CO_2$, which we understand pretty well why it's there, and a little bit of a lot of other compounds, which we don't understand very well."