I know what you mean, and this has been a very frustrating issue for those of us that manage multiple desktop pools within a Linked Clone "Refresh immediately" environment. I'm not going to disable provisioning or change the refresh setting of the pools back and forth during recomposes as I still have to babysit recomposes, and this creates a terrible amount of administrative cleanup and maintenance.
To be quite honest, I don't think VMware originally forsaw the amount of customers that would use such features. However, being able to recompose a pool on the fly and not disrupt existing users to push out updates or new installs on master images is to me an incredible feature. We are a Healthcare organization and simply cannot afford to take Desktop downtimes to do this.
I can tell you this, the last time I spoke to support regarding a different issue, I brought this up as well and was told they are aware this is in an issue for some of their customers. Our organization also has someone that sits on the Beta for View and has been hammering on getting some sort of feature in place to set recompose to trump refresh. I know VMware is responsive to such concerns, because one of the things that did come through the last View release that we pushed for was the "Minimum number of ready desktops during Composer Operations" so that recomposes wouldn't just chew through all available VMs in a desktop pool before readying other replacement desktops.
