Granted, an in-mast furling system doesn't allow for a great cut or shape to the main but it's a no brainer when it comes to reefing or furling. When the S--t hits the fan and you're running around in a hurry it's difficult to screw up, but,, not impossible.
I'm not in the loop of furling booms as we don't have one but (from others experiences) I would think that there would be a better chance of having a problem with a furling boom.
An example might be when you're in a broad reach with 15 knots and it picks up to 25 or 30. You decide to reef while continuing down wind and start furling. I've done it with an in-mast furler and it was no problem. We slowly furled it 50% and kept going (same with the headsail). I don't know about a furling boom. Just seems like it would be easier to jam or give you trouble under those conditions. I guess you could just grab it and pull it down but the idea is to keep the boat moving under control.
Then again,,, I have no idea as I don't have one. We like a standard hoisting main.