NO, NO, NO, just NO, have i already said NOOOO?
Of couse you choose. You decide you want to be able to do farming and therefore want to skill "Living of the land". Because you WANT to have "lotl" you need to skill fortitude. But with that decision come two options:
1. you are "forced" to use machine guns and/or knuckles if you want to take advantage of the skillpoints put into fortiude
2. the points put in fortitude are completely wasted because you don't use machine guns or knuckles
All that just because "lotl"? Why should a farmer not use shotguns or whatever?
You want to build an undergroundbase and therefore skill miner 69er? There you go, you are forced to shotguns and sledgehammers because of strength or need to invest in for yourself useless skillpoints.
You want to use a shotgun but for melee prefer blades? You're welcome, you need to invest twice as many skillpoints to get both weapons good in opposite of using shotguns + sledgehammer or pistols + blades.
So in the end the only thing you choose is "do i play like the skillsystem tells me to do but efficient" or "do i play like I WANT, but waste a lot of skillpoints for being able to do so".
WTF!
I'm really not trying to troll you, but it does seem as though you are
choosing to see this in the most negative possible way.
You haven't 'wasted' the points; you've spent them to get access to Living off the Land, and - as a bonus, it has made your fists and machine gun get a bonus. You can
choose to take advantage of that passively by using your fists or a machine gun, toy can
choose to optimize it further by perking into the Brawler or Machine Gunner perks, or you can
choose to use any other weapon you want, and perk that weapon later.
None of these
choices involves wasting the points into Fortitude, it's just how much of an advantage you chose to make of that path at that time. Your clubs, hammers, spears, machetes, handguns, shotguns and rifles remain effective - and you can make them more effective by
choosing to perk into them later.
Which you prioritize is up to you. When you perk them is up to you. There is no level cap - it's just a matter of how much time you put into it. The farmer absolutely CAN use shotguns or whatever, they just won't be OP. I'm not sure you are appreciating how OP weapons become when you are fully perked - and how effective they remain even when un-perked.
The only thing you cannot do is get everything that you want from one skill tree.
So in the end you
choose every single aspect of what you perk into and when - and you
choose to play how you like - but you don't get to be OP in every single thing you want without a substantial investment of time and effort.