Where you start running into problems is when you want to let players define the game they want to play or where you want to run a game outside the box.
That is a "problem" only if you require one system to be all things to all people. I don't. I play lots of different games. If my players want something D&D doesn't handle well, I use a different system.
And, despite your assertion otherwise, no, I don't need to know exactly what game is going to result in order to choose. I only need to know generally. And of course I have sufficient discussion with my players to know what it'll be before we get to character generation.
Your position becomes very unimpressive if it contains doses of such assertions of things I supposedly must do, that I have gotten along for decades not doing.
Or any number of other things where you have a major component to gameplay that isn't dungeon crawling where mundane every day life isn't so mundane and is in fact pretty dangerous and potentially fulfilling as an adventure fantasy.
I begin to suspect we are referring to different things with the phrase, "mundane, everyday life".
I'm talking about the stuff that everyday people in the society do on a daily basis to get by - growing or creating food, manufacture of consumer goods for sale, the raising of children, and so on. These basic things must be low-risk, easily accomplishable tasks, or you can't have a reasonably stable society in your world.
I don't care if you commute to work by getting on a 20th century bus, or flying on a pterodactyl, or by picking up a pointy stick and going to dig for tubers - the bulk of the population must have very little problem doing it, or you lose a significant portion of the population every day to trying, and your fictional society falls apart. Broadly and statistically speaking, going to work in the morning must be pretty much a no-brainer.
If there isn't going to be a significant consequence and notable chance of failure, you don't need to roll the dice, and you aren't going to need mechanics. "Life skills," are things that generally succeed, and therefore don't need mechanics.
If you want to introduce complications in mundane life events, there are ways to do that without having so many "life skills" built out in detail.
... or perhaps more importantly, that the same long running campaign can't feature all of the above based on player choices at different points in the campaign. Because you know, I've been in a game that diverged across that many different types of gameplay in a single campaign/story without necessarily all of them being planned by any one participant (including the GM).
You've presented them as if they were entirely different forms of gameplay, when I am not sure that was necessarily the case.
Like "flying between asteroids" is not a fundamentally different type of gameplay than "sailing between ports". And the only real difference between pirates/bandits and merchants is whether they steal or buy their initial trade goods, and maybe not even then.
The items that stick out are the stone age scenario compared to, say, the feudal lordlings one. But therein, the issue is not that the system involved would not have the full skillsets for each, but that you'd not expect the characters to have the skillsets for both at the same time to begin with. The wannabe French Dauphin isn't going to know how to knap stone tools. I don't need to have a skill-system for a skillset the characters don't have!