Regardless of whether or not there's an agenda in that article, the reality is complex. Obviously, even if riding an ebike has a lower carbon footprint than regular cycling, carbon emissions are only one type of pollutant. The other pollutants in battery manufacture are no less of a concern. Equally, much depends on the type of food consumed by riders and how it's produced; after all, some forms of agriculture are more damaging than others (and again, not solely as a result of carbon emissions). Likewise, the carbon footprint of an ebike depends on how the electricity that's used to charge the battery is generated.
To be fair, the author of the article is clearly aware of these issues and he's very candid about the limitations of the comparison being made, even saying that one part is 'simplistic' and that another is 'UK-centric'. However, what has been shown is no more than that, given certain assumptions, ebikes could have lower carbon footprints than regular cycling. The article doesn't consider overall environmental impacts and how they are affected by varying the assumptions (but doing that would be more like a PhD thesis than an article for mass consumption!). It's food for thought rather than conclusive.