We know that the shakkan that Briar steals from Crane is an incredibly powerful tree. It’s age has given it an intelligence that is unusual in plants and it is a storehouse of power that Briar (and, presumably other plant mages) can tap. It saves Briar’s life four or five times over the course of the books. But Crane gives it up for just one tomato plant. Sure, the plants are nearly impossible to grow in Emelan and thus incredibly rare, but they aren’t magical artifacts. The tomatoes are valuable, but the shakkan is priceless. So why did Crane agree so quickly?
I think it was because he knew he was in trouble.
Crane is a great mage, but we don’t know much about how his magic works. He definitely can’t hear plants the way that Rosethorn and Briar do, or he would know that the shakkan is 146, not the 130 he claims (each year likely adds more prestige--no way Crane would round down). He certainly uses plants in his magic, and is likely famous for how he works with them. We don’t hear about Crane owning other shakkan, which means this was his first. He had probably heard their reputation -- Rosethorn describes shakkan as vain and demanding-- but he also knows what a status symbol they are. What a fine centerpiece for his magnificent greenhouse! But once he installs the shakkan, things start going wrong. It isn’t happy and it isn’t healthy. It has brown branches.
Crane is arrogant, but not stupid. He doesn’t know what’s wrong with the tree, but he knows he is in over his head. Rosethorn points out right away that the tree is in the wrong shape and the wrong pot. Crane had no idea of this. He only knows that his tree that was supposed to be a symbol of status and his own abilities as a mage is now sick and possibly dying. A dead shakkan is an unacceptable blow to his reputation. He can’t ask Rosethorn for help without losing face, but he doesn’t have a lot of other options either.
Then, Briar comes along and steals it. Crane is indignant at first-- how dare this little rat steal from him! And on Rosethorn’s orders (presumably)! But then Lark starts to help him to calm down and think rather than react, and Rosethorn offers him the tomato deal. Sure, the plants are not a fair exchange, but a rare plant for a dying shakkan is a very, very good trade.
Crane saves himself from the embarrassment of having a dead shakkan, he gets a tomato plant and he looks like he’s the bigger person in the agreement, since he is accepting the “lesser” payment. He still doesn’t get along with Rosethorn, and his classist biases prejudice him against Briar, but he is secretly very, very pleased that Briar stole the plant.