I mean just from what I've personally seen:
1) DSOTM black black, came with a 1/4 worn AR coating. Denied warranty and made the owner service it at his cost (~$1400?).
2) SMPc with serial number removed. Denied warranty and made the owner service at his cost (don't know what case middles go for, but that's a big number in addition to waiting for them to serialize it for him).
3) gen 3 PO with screws that were chewed up prior to him getting the watch. Told him to just go to Omega to get new screws. He got them, but a pretty crap experience.
I personally would never used JS on a watch costing over $1000. There are too many good dealers on the forums that you can get almost any watch BNIB or LNIB for so close to the JS price WITH warranty cards that it's not worth it.