A setup action is the same as any other action roll – you judge its position and effect based on the fictional situation. They might be different than the positioning of the roll they’re meant to set up.
If a setup roll is possible, it’s likely going to be standard effect (we’re saying the character can set up their ally by taking an action in the fiction) – but I wouldn’t say that’s absolute. Maybe it’s great effect, and there’s more gained than just altering position or effect. Or, maybe it’s limited because shifting the situation will require a great deal of teamwork or time.
Say the crew is fighting Lord Scurlock in his mansion, and the cutter wants to throw it all on the line with a desperate Skirmish action, but the GM looks at the situation and says, “I think it’d be a base of No effect… just a few factors: he’s got serious arcane protections here in his home, he’s much higher tier than you are (he has centuries of experience and his mansion is full of implements and weapons he could use against you), and he’s a vampire. Unless you find a way to equalize his advantages, you won’t be able to harm him.”
The whisper says, " I want to do a setup action to Attune to those arcane protections you mentioned, to find them and alter their purpose so they magically attack Scurlock and distract him instead of defending him."
The GM might say, “Cool! Sounds desperate/standard to me. If you succeed, the wards will shift their purpose and begin to send out shadowy tendrils to bind Surlock’s limbs. That will give the cutter some level of effect.” This choice will keep the action moving and be simplest.
Another option might be to say, “These wards are beyond the studies you’ve made. You understand the concept of them, but you’ve never seen something so devious. You can try to alter them, but it sounds like a desperate/limited roll to me.” The player has many options then. They could accept that it might take multiple rolls to achieve their help action, or they could push for effect or flash back to change the fictional position somehow.
If they do decide to take their time (rolling at limited effect), the gm might start a “Wards” clock. Maybe Scurlock acts (as a master NPC and/or from roll consequences) while the whisper is frantically attuning, and the cutter is left to resist his attacks (or protect the whisper if Scurlock notices their tampering). Maybe the crew’s hound joins the whisper in a group attune action, hoping one of them could roll a crit (which would give them increased effect).