I've received estate pipes many times where the stem was removed, and it hasn't resulted in any issues. But, I do know what you're talking about, and I always leave the stems in place, at home, when shipping, and once in a great while take them apart for cleaning. I've seen interviews where some well known pipemakers have said exactly what the OP said, and for the same reasons. Basically when the pipe is finished being made, at that moment the stem/shank fit is as good as it will ever be. Taking it apart and exposing it to possible changes in temperature and humidity could cause the wood to swell, shrink or somehow warp. I understand the reasoning, so I keep them together...but, like I and others have said, have not had an issue when a pipe has arrived, both pieces not attached.