To such an extent that being a QB from a spread or heavy-shotgun college was seen as detrimental for a draft prospect even just a few years ago...analysts would talk endlessly about how hard it would be for a QB to adjust to a "pro-style passing offense". There was a
lot more to that than just shotgun vs. under center, of course, but it was part of it; analysts would talk specifically about the difference between passing from under center and from shotgun as if being used to passing from shotgun was an impediment.
If they saw passing downs as probable shotgun downs, why make that a talking point?
It's all still very much in flux....the first time the league aggregate numbers were heavier for shotgun was 2013, and it's been slowly taking over on running as well as passing downs since. If you look at that chart, the aggregate 1st down usage honestly was still predominantly under center as recently as 2017, while the aggregate numbers were higher for shotgun.
It's recent enough that for all we know, it could still flip back the other way as coaches continue to react to each other and innovate...the NFL is an arms race, and in 3 years, we could be right back at an under-center norm.
All we can really do is deal with where we are right now...and "right now" is a shotgun-centric league. Conventional wisdom is going to cause some people to miss that, or dig for edge cases and reasons the trend isn't really a trend...we see behind-the-curve coaches and executives do that all the time. Human nature is to be comfortable with what we already knew.
But as it regards Madden, shotgun formations in Madden 20 are so prevalent because they're more prevalent in the league at the time Madden 20 was made. It's really that simple.