From a normal daily calorie expenditure only a fraction goes on physical movement. The greatest share goes on cell biochemistry, followed by digestion, then normal stuff like heart beats. Additionally all the physical movement like rolling over when you sleep and reaching for a coffee. This means that for most people an hour work out will add less than 10% to your daily energy expenditure. And your body can naturally reallocate energy from different processes if you are in deficit. Like running some other things in a slightly lower energy mode.
If you are in a serious deficit for a long time it can be harmful. But the more immediate worry is getting the right things at the right times.
If we step back and look at this as a problem of abstraction. An advantage of abstraction is that the people working at the higher levels of the abstraction don't need to know what is happening at the lower levels. Therefore people can specialise and we can achieve better efficiency as an industry. If everyone needed to understand everything we'd be screwed.
In reality there are abstraction that work very well. You don't need to understand the internals of python to use it for example, though you may be able to use it better if you do. C however I would argue that you do need to have a mental image of what is happening to use it.
Also the operating system. People use that all the time without knowing how it works.
Maybe we are just at that early in web dev and we are waiting for the Unix of web frameworks to arise. Or perhaps there is an inherent tension between the developer needing to fiddle with the details while the framework tries to abstract those details away.