CO2 is damaging to your body, I am not an expert in these matters however I know that much.
Becoming tired due to CO2 is in effect a minor form of gassing yourself, and during sleep high CO2 is bad for you and I would assume does not give you high quality sleep - same as alcohol makes can make you drowsy while also interrupting your sleep.
"Natural" sleepiness has none of these downsides.
Most of the claims are trivially verified true with a proper understanding of hypoxia and the effects on the brain.
Of course you want to be sleepy, but you don't want that sleepiness to be due to hypoxia because hypoxia is known to damage the brain.
The link you gave makes me think I actually have to dig through quite a few studies to find something supporting what you said (it's not on the first page, for anyone wondering), which is why I asked for direct sources.
A simple search of "hypoxia from excess CO2" brought up https://en.wikipedia.org/wiki/Hypercapnia, which also support the claims.
Please, for the love of god, learn to google properly: http://www.catb.org/esr/faqs/smart-questions.html