A 7–9 on Tricks of the Trade is a game of “Would You Rather?”, with the GM asking the question. “[T]he GM will offer you two options between [three options]” means that the GM will be selecting two, and then offering them to you as options, so the end result is the Thief choosing one (but the GM having input too).
But it's more than simply a way for two participants to have input into picking one from three — this structure passes through the GM's Agenda and Principles, so there's a transformation after the GM's choice and before the Thief's choice: the GM picks two, crafts a dilemma out of them, and presents the in-fiction dilemma to the character.
That last bit is what makes the move sing: the GM should make these real situations that require a choice, not just “uh, choose danger or cost, then I'll make something up.” It should be more like
The rest of the party is past the pressure plates, so it's your turn to get moving, but now you realise you're not sure you can extract your toolkit from the mechanism under the plate you levered up without priming the rest of them again. You could leave it behind to permanently jam it, or extract it and take the risk that the pressure plates between you and the rest of the party might be live again. What do you do?
This is a natural result of following the GM's Principles to Address the characters, not the players and Begin and end with the fiction, when combined with the text of the move.