Is it really possible to mix pools for different coins?
I know that you can e.g. solo-mine in cgminer and leech the new block info from a pool. But that would assume that the pool config in cgminer refers to a single coin! Otherwise the new block info is bogus.
Does anyone know whether this is a problem and if so how to get around it?
I think you're right. As you described, the behavior wherein cgminer uses stratum/longpoll notifications from backup pools would cause cgminer to erroneously think that blocks have changed over when they haven't. I don't see any way to disable this behavior and in the very start of the cgminer readme there is the message
"Do not use on multiple block chains at the same time!" which seems to be an acknowledgement of such issues.