A good wipe with a paper towel is supp9osed to keep cake at bay. I wipe and use the knife now and then. The color you see in the bowl after a wipe or scrape is what is migrating to the outer surface.
The bowl warms, the wax softens, and you'll feel it. Clean hands are a must. Cotton handkerchiefs or gloves are optional, in my opinion. Your hands are more likely to move the surface wax around. A clean soft cloth will do the same and not transfer dirt and oil from the fingers. Again, this is strictly anecdotal on my part as it relates to my pipes and experience. I prefer to handle a new meer by the bit, when warm, as much as possible. After a few dozen bowls I become a bit more careless.
The porosity of each meer will be different and color differently. No guarantees of anything with meer, it is mineral certainly to be full of peculiarities.
The pipe to me is a tool. It will get dinged a bit over it's lifetime, changing color as it ages, provide many hours of enjoyment and, eventually grow into a trusted, highly valued smoke. All of this if you are careful and were lucky in your purchase.