You make excellent points and I did not really believe that anyone would actually try to earn an entire level and thus secure a point by only doing the one xp earning action that most aligned with the perk they wanted to buy. You are correct that you would have to plant and harvest thousands and thousands of crops if you decided to start being a farmer at level 120. I just stated the fact that the option is there for purists who really want the xp for points spent to come from well aligned actions that earned those points.
What I am really getting at is the argument that many people use to say the perk purchasing system is bad (that being that points earned are incongruous to benefits gained) is not a foregone conclusion. The middle road is to impose upon yourself some practice--enough to feel justified in having earned the right to spend the point in that area. I'm at level 120 and after a huge screamer horde am able to get to level 121 and have a point to spend and feel like doing some farming. If I really felt that learning by doing was fun and immersive then I could spend one day planting and harvesting and doing farming actions before spending the point. Did all the xp come from that? No. But I'm playing the game the way I claim to like and I reject the notion that putting off spending that farming point by one day to do a bit of roleplaying automatically disqualifies that gameplay from being survival gameplay. I also reject the notion that because the current structure allows for roleplaying to capture the feeling of learning by doing that it makes it a weak structure. I think forcing a quest to practice actions before the perk point can be spent would make for an interesting mod but forcing players to learn by doing without the min/maxing powergrind component included would not be a popular thing for the default game because lets face it: the min/maxing powergrind component is the real candy that those players crave and "learning by doing" is just the excuse.
TFP has indeed made their choice and it is against automatic leveling and I'm just offering up a solution that can help those inclined towards role playing. Obviously min/maxers aren't going to apply.
Now as to your points about perks I too hope that TFP gets there. There are fewer incremental percentage perk trees than there were when Joel showed the videos because he does want the perks to grant abilities and be more interesting too and he did rework some. Hopefully the remaining uninteresting ones will get replaced with abilities like kicking or stomping etc...
In the early game, you have to do all kinds of different things and in the later game, it takes very long to level up, so to restrict oneself to do only or mostly one activity between two level ups, is unrealistic as well. There might be a window when your "solution" makes somewhat sense, but even then I couldn't see it as "roleplaying" to restrict my gameplay in a way so I can align it with a perk I buy.
Who those purists are, you talk about, I don't know, myself I don't care about "min/maxing", I (simply) find any gamey game mechanic unimmersive. Like a zombie's health bar or upgrading a wooden block to one that suddenly does not contain any wood anymore or chipping away "wood" after "wood" from a tree, until a "tree" stands before me, that consists of no more "wood" than I need for one arrow.
Besides that, I don't see a reason why I should not get better at something if I do it over and over again, just because I do not have gamey game points left, or why it should take five minutes to improve a skill in the early game, but an hour to improve a skill in the late game (of course I do understand the basic reasoning behind the curve), or (and that's the classic your "purists" seem to complain about mostly) why I should be able to level up my archery skill by gaining experience by breaking down boulders with a stone axe.
What are the reasons for perks again..? That you are free to level up your archery skill by gaining experience by breaking down boulders with a stone axe, right? That "freedom". And getting that monkey off the back of compulsive "min/maxers"? Or denying them their.. "evil" or "wrong" playstyle..? And that a perk system sorta kinda resembles Fallout, a game Joel likes..?
Ok...
Surprisingly, I assume that the system will reduce my freedom. Currently, I can do what I want. I'll always level up my skills and level them up reasonably fast, no matter when I start using them. With the perk system, I have to plan ahead. I might, in the early game, not intend to build a base from scratch. But maybe I'll decide that later, so I have to either set points aside to use them on the corresponding perks later or buy perks I don't currently need, because I might need them later, or get ready for a serious grind because later, leveling up will be terribly slow.
Again: For what? Why is a good system removed? To stop min/maxers? I find that absurd.
Perks are good for games that allow and require from the player to build very different characters. With very different abilities, that play very differently, but still get the job done equally efficiently. Another good example, possibly a better one, besides Skyrim is the perk system in Path of Exile. Sad, very sad, actually, that it's not in first person. In PoE it even makes good sense to mix those "deal 1% more damage" perks in, as you build your character along an actual "path" of perks. Nicely done.
7dtd does barely allow you to not use an ability the character has. And so far, there are hardly any abilities in the game, that not every character has on the first day already. Those combos (hit 5 enemies in a row and you'll deal some extra damage to the last) remotely resemble the principle, but really, they are not an actual ability of their own. Other than that, you don't need to farm and there are a couple of things you don't have to craft and you don't have to use certain items and blocks, such as certain weapons or electricity.
Edit: Btw, I have a great solution for the issue. Wanna guess what it is? I'm sure you can easily figure it out.
Here is a second edit: This just occured to me when I was, you know, "in the office". Doing "my business". Min/maxers.. Can't they still min/max the crap outta the system..? Spam craft, put a weight on the mousebutton and beat on a block with a club or a stone axe? Level up much faster than the naturalist? I'm sure they can. So for the min/maxer, wouldn't the perk system, instead of a problem, actually be min/maxing heaven? Cuz now they can min/max whatever skill they want with the most efficient activity. If, for example, crafting stone axes would be the most efficient way to earn XP, they could not only just level up their stone axe related skills, but all of them.
Eh?
To stop these guys, you could design it so that you don't get points based on XP, but time. Give points after so and so many minutes and make that a curve. First point after 5 minutes, next one after 6, then 7, and so on.