It might be too early in the AM for me; I can't discern when this noise is happening for you. Does engaged mean the clutch is engaged or the clutch _pedal_ is engaged?. Commonly, from a mechanical perspective the clutch is said to be engaged when the clutch pedal is up, but I don't think that's what you're describing.
i.e. Is this the case?:
- Transmission in gear & clutch pedal up: everything's fine
- Transmission in gear & clutch pedal down: everything's fine
- Transmission in neutral & clutch pedal up: crazy noise
- Transmission in neutral & clutch pedal down: crazy noise goes away
Without other data, if a bad noise goes away when you push the clutch pedal down, it's likely not the slave or master cylinder.
- If a bad screeching noise starts when you push the clutch pedal down, it's likely the throwout bearing.
- If a bad screeching noise starts when the clutch pedal is up it's likely the flywheel surface, the pressure plate, or a clutch failure (e.g. broken/out of place spring)
- If a bad screeching noise starts only when the transmission is in neutral and the clutch pedal is up, it is likely the input shaft bearing.
- If it's hard to put the transmission in gear without grinding, or the jeep tries to move with the pedal down, it is likely the slave/master cylinder/pivot arm.
Obviously those aren't 100% diagnosis statements, so there could be some information the shop has that we don't which points to the slave/master combo.
FWIW, the slave/master can be purchased in a combo kit pre-bled with fluid, and replaced in about an hour or so if you are familiar with the jeep, and is how I would recommend changing it.
Lastly, the TJ flywheel is not really designed to be resurfaced. Many shops I would otherwise consider competent don't know this and resurface it rather than purchasing a new one, which can cause several issues, clutch chatter being one of them.