I editorialised the title as the original was clickbait, but the video itself is quite good. Interestingly, e-bikes are claimed to have lower emissions than acoustic bikes, although it likely depends on diet (the author didn’t specifically compare a vegan diet between the two types but did indicate that vegan + electric is the most carbon efficient form).
You’re right that the calories burned while riding the E-Bike would also need to be considered. The site you linked gives 220 kcal/hr for “Motor scooter, motorcycle” and 630 kcal/hr for “Bicycling, 12 - 13.9 mph, leisure, moderate effort”. This corresponds to 1960 kcal / 100km excess calories for biking (at 75kg weight). Going slower than that (which I certainly don’t do ;-) ) somewhat reduces the difference. But then the E-Bike is faster and you somehow have to account for that… I’m sure that people have written scientific publications on such considerations. My napkin math certainly doesn’t have that level of rigor.
Overall there’s certainly better ways to reduce your CO2 footprint than switching from a bike to an E-Bike. But perhaps E-Bikes are better than their reputation.