I've had a few putters customized from the custom shop and a few by other places. The quality from all have been amazing and about equal. The CS is MUCH more expensive. I only use the custom shop when I might want to sell the putter later. I had a few things done to my button back and still have it. If you want specific scotty stamps or headcovers, the custom shop is the only place to get it. But they are also generally limited in finish or stamps or placements. If you want some cool finish or different stamping or engraving, there are plenty of great sources.
I have 2 good examples of different refinishing/customizing. The first one is a Mizuno Betti with a BOS finish that was all beat to hell and back before refinishing. The second is a classic oil can newport that went to the custom shop for a pro platinum finish, a stamp and top line. It was not as beat to hell but it was dinged up a lot.
Mizuno Betti:
Classic Newport: