I think in addition to the misunderstandings, is that cycling (and swimming) simply allow you to go too easily if you choose to.

Going at hard efforts is painful and potentially injurious (but pretty hard to do so on nonimpact cycling), but increases your baseline metabolism by the adaptations required to ride at those hard levels. More muscle, more capillaries, more efficiency, etc. Riding easy all the time might burn similar calories if you cover simiilar distance but it won't bring you those baseline metabolic increases anywhere near as much as if you went hard for the same distance.

Running since it's weight bearing, seems to automatically push you into at least that baseline metabolism increasing effort. It's why running can be so painful to a new person, but also why it's pretty unusual for any decent runner to be even mildly fatty - the fat tends to fly off with running with the baseline metabolic changes in the legs. It's not because of the megamiles run - cyclists routinely put in more calories burned than runners of similar ability, but the impact per stride is so high in running that even leisurely runs cause a significant baseline metabolic acceleration. (I run sub-6 minute mile 5ks, but I train at 9min/mile, and it still improves me. I'd never improve on a bike with that sort of a pace gap.)