Cardio lowers risk factors toward ill health. If bodybuilders had to show their heart muscle in a contest they would train the hell out of it.
The more cardio you do the lower your resting heart rate is. That shows your heart muscle is more efficient and stronger. Cardio lowers blood fat in the form of triglycerides. Cardio lowers visceral and subcutaneous fat. People can increase their HDL lipids by doing regular cardio. It can change the HDL to LDL ratio. Cardio increases red blood cells that carry oxygen. It can lower high blood pressure. Cardio clearly lowers blood sugar in most. There are other risk factors it can lower. Guys that don't do any cardio are shocked at their lack of endurance when they box or grapple for the first time. I've seen bodybuilders after boxing 2 minutes can't keep their hands up due to exhaustion as the skinny boxers go to town on their their cosmetic opponent.
Regarding Nautilus there was a good study that showed after 12 machines most trainers barely used 100 calories during their workout. Increasing cardio capacity was another failure. Apparently the spike in heart rate was too short to significantly increase cardio capability. Medical doctor Ken Cooper is a legend in exercise research concerning lowering risk factors from the lack of exercise. Of course genetics trump all. The other Ken is a chiropractor back cracker. Not a scientist.
You bring up some excellent points that merits consideration and debate. One of the things Jones did for me, and many others, was to think and reconsider the various theories being promoted at the time, mainly through the muscle rags and bro science you would find at your local gym. With no internet and little, if any, serious books on the subject, this is all we had. Jones offered a different perspective backed up with logical (at least to him) arguments and real world experiments and left to the reader to think it through and ask himself, "Does this make sense?" That is what I would like to do here.
First off the blanket statement that "The more cardio you do the lower your resting heart rate is." is simply not true, and, so not true that I really don't want to argue the point much other than to say that any blanket statement that states "the more you do the better the results" just doesn't pan out in real life ever as diminishing returns, indeed, regressive returns, is always the end result when taken to it's logical conclusion. One can literally run himself into the ground and even to death when taken to extremes. But perhaps I am taking your claim too literally.
The heart operates more like an organ than a muscle, which we tend to associate with the class of skeletal muscles. Like organs and unlike muscles, it does not get stronger and more efficient with use any more than say your kidneys or liver and even your lungs. It gets worn out. The contractile force and the size of the heart is predetermined at birth. For the contractile force of the heart in general to increase and get stronger it has to get bigger, just like your biceps, and to some extent it does but only marginally so as it is limited to the size of your chest cavity. Just like your lungs. Your lungs can only get so large to increase oxygen volume but only marginally due to the limits of your rib cage size.
So though the heart, per se, doesn't increase much in strength and efficiency your cardiovascular system as a whole does. Increase size of arteries and veins, capillary and blood vessels, though individually is quite minute, taken in totality it makes a huge different. Blood and oxygen transfer, in addition to an increase in red blood cells, is vastly increased resulting in better conditioning and not the strength on your heart any more than the size of your lungs increase oxygen transfer.
Now, it is quite true that a bber will gas out in the ring when compared to a skinny boxer. But how will a boxer fare if required to squat his body weight? Can a 200lbs boxer squat 200lbs or even 150 pounds for fifty reps? I witnessed Benny Podda at 225lbs squat 315lbs for 50 reps. The average person can't do fifty reps in the squat with just his bodyweight. I would deem the chunky 5'5" Podda to be in pretty good condition compared to the average Joe and even the average athlete in regard to functional ability.
The point being is that I have found, both in personal experience and observation, is that your body is very activity specific. Meaning that extensive strength and conditioning in one activity is not proportionately transferable to another activity. We find this in strength training. At my best I was able to do 315lbs for six reps on the bench. I then stop benching for around nine months and instead did bench on a machine or used dumbbells instead. I increased the weight, and presumably strength, substantially on both movements but when I went back on the bench I could only squeak out 3 reps. Did I get weaker? I mean, my body weight was a bit higher and the weights I was using were greater in those nine months, yet my bench went down. Was I weaker or just "out of practice" in benching?
I had a training partner that I introduced to Jiu-Jitsu and I always considered him in superb physical shape as he was a marathon runner. At that time I felt marathon runners were the epitome of cardiovascular fitness. I mean, running 26 miles? At the time driving my car that distance I considered iffy.
Anyway, much to our surprised, this marathoner found himself gassing on the mat. He could not keep up with me. This was puzzling to both of us but at the time neither of us gave it much thought. We were on different schedules and didn't train much together but two years later we met up again. He was a much more formidable opponent this time around and his conditioning was superb and I found that I was one the dragging. We joke about the time two years earlier when he couldn't keep up with me despite being a marathon runner. He then told me that he gave up marathon running and there is no way now he could get through a marathon. He said he cut his running way back and nowadays even an 8 mile run was taxing. Yet he was tireless on the mat.
Did he lose cardiovascular conditioning or was he just out of practice running?
The legendary wrestler Dan Gable, know for his superb conditioning, was once asked what was the best exercise to improve one's wrestling condition. He replied, "Wrestling."
Perhaps there are other factors involved other than pure cardiovascular efficiency that determines one's stamina and condition as it pertains to a specific activity.