I'm not able to come to anything conclusive about Gardening, Fertilizer, and just what makes these harvestables come out more expensive. I think it's random and buggy at once just buggy. I experience the same thing while selling harvestables in that if I sell them one by one, I can make the prices of others go up. Quite an exploit when you're talking about something like Blackberries with a huge value.
I did testing with Apple trees, knowing they can produce $33 fruit. I harvested one each day, and got $13 apples each time. That is a huge difference in what IgnorantBliss experienced, given the Apples were worth $23 by day 3.
After selling some of my Pomegranate to test the sell-one-at-a-time bug, I saw my apple prices fall. What were once all $13 fruit became a mixture of $13/$7 fruits.
My UFO prices cut in half, all of them. At one point, there were plants worth $408, which became 204 while others went from 120 to 60. This happened a second time when selling some plants.
Given all this, I can't say definitively what is supposed to be happening here. I figured they would come out randomly giving us different prices each harvest, given that no two apples are alike. Instead, we sell them and the prices of others are manipulated. If you sell the highest one you have when doing this one at a time thing, the price goes up on all those of the same value. I got $83 apples exploiting this and could have kept going, they just kept going up $10 each. Sell off all the low ones, then sell the next highest, and so on and so forth and you'll eventually have a massive inventory of ridiculously priced plants.
I am going to file a bug report if it's not already done. I can say that it's not time on the plant that makes it go up, because I had an apple tree going 10 days without harvesting that yielded $7 fruits. I think that selling fruits affects the prices of the ones still on the plant in your lot. Seriously whacked out system here.
Edit: It doesn't matter how the plants leave the inventory - if they are stored in the fridge, sold one by one, used in meals, OR PLANTED they will affect others of the same price. This is why people get wildly different results. When you plant them, you do it one at a time and suddenly see you have $83 apples that are meant to be $13. I now believe my first values are the only values we're meant to have and the plants changing value is just a bug.