I see what you're saying, you'd prefer the semantics of it were the other way around: that when Apple decides to enable such features by default, that they enable them internally but change the options to say "Disable Constant Properties" and "Disable Viewport Fit" and for those toggles to be off by default. So the result would be the same, but all the toggles would be off by default.
They could definitely do that, but the reason they don't is to provide developers with consistency during the process of these features being introduced into Safari. They start off by adding features and having them disabled by default, then once they're considered stable and ready for widespread use they enable them by turning on the preference by default, then eventually they bundle the behaviour in and remove the preference completely. For the sake of consistency and simplicity the behaviour of the menu (in the case of macOS) or toggle (in the case of iOS) is always left the same throughout that process, so that people who are actually working with these features on a regular basis don't have to keep adjusting to changing menu and toggle behaviours. It would be annoying to reverse the intent of the menus and toggles with different point releases when there's no reason to, especially since these preferences are not intended for the average user to be worrying about. That's why they're placed where they are, with the menu hidden by default on macOS, and tucked away in the bottom of Safari's "Advanced area in a section called "Experimental Features" on iOS.
And, back to the original topic of the thread, there's a reason why they're put out of the way: so that people who don't understand what these features do, don't go messing with them and then attributing non-existent benefits or disadvantages to them, spreading incorrect information that's going to make things worse for themselves and others.
I'm sure Apple would prefer the options were even more hidden for this reason, but they've done a great favour to developers who do need regular access to them by placing them in a directly accessible location - this is especially true of Viewport Fit, where it's extremely handy to be able to quickly turn it on and off while testing layouts on iPhone X.