The pipe material is definitely part of the chemistry. Keeping to one material, like Meerschaum, briar, or cob, definitely gives more dependability on how particular blends taste. You can learn to pair different blends with different pipe materials, and most of us notice how cobs favor certain blends and kinds of blends. But it stands to reason.
I don't want to be Chicken Little, but I've read some warnings that smoking clay pipes with clay stems is not a good idea, and some of the clay pipe makers now at least wrap the bit in plastic to shield the lips from the clay. Neoplasms on the lips (irregular cell growth) is the suspected problem. I don't think there's research on this, since the health community recommends not smoking anything. Probably a plastic bit or covering is a good idea with clay pipes, especially if you smoke them regularly.