What kind of yamaha? What mounting? I have a yamaha completely rack mounted, with the minimal contact yes mounts and they sound great and really resonate. No modification necessary.
I have a Maple Custom Absolute kit with Nouveau lugs. I can hear a very noticeable difference in the 10" and 12" between my tuning them and then mounting them on the YESS mounts on the bass drum. I am pretty careful to not run the hex rod all the way through to the shell, but I still hear it choking somewhat. So that is one issue. The other is that now my technicians have to keep up with an additional set of mounting hardware for that particular kit as opposed to just using "L" arm mounts like we do on every other kit in my inventory. Standardization is key to quickly getting gear ready to go on the truck and also to not accidentally forgetting something thus having an upset client.
The only reason I have not installed a couple of isolation mounts already is the nouveau lugs are tough enough to deal with as it is. I am not entirely sure how much fun they will be with an isolation mount. We change a LOT of drum heads around here!
Johnny, you are correct in that vintage drums do not have as much sustain with a round over bearing edge, but I do notice a difference in the tone of the drum when suspended vs. standard mounting techniques. I also hear a distinct difference when using air cushion feet as opposed to standard feet. That isn't everyone's preferred sound, but I always start there and then dial it in for a specific application. Over the last few years the trend has moved back to pretty dead drums. Not just vintage drum sounds, but "dead" drum sounds. I have some ideas as to why that has been happening but I will leave that for another day. I can always deaden an open drum, but if a client is looking for a more open tone I sure don't want them to tell me the drum sounds a little choked to them.