Yes, muscles definitely increased. My upper legs became more muscled which I could simply measure by the fact that I didn't fit in my jeans anymore. But at the same time, belly fat remained roughly as pronounced as it was before exercise.

The whole "exchanging fat for muscle" thing is wildly exaggerated. It really doesn't happen to any significant extent. You'll put a little muscle on your legs from cycling but at most probably a pound or two. When people claim they stayed the same weight but gained muscle, it's mostly wishful thinking. It's hard to put on significant muscle even when exercising specifically for that goal and intentionally gaining weight. It just doesn't happen accidentally from cycling to work.

Do you drink much? Anecdotally my friends seem way thinner shape once they cut out beer, maybe even alcohol entirely.

Studies leave it out because it's such a minor effect. You won't put on a meaningful amount of muscle from cardio. It's just wishful thinking when people see their weight stay the same and assume it means they've gained a bunch of muscle. Meanwhile their pants don't seem to fit much different... Lots of stomach muscle, I guess.