Welding prep, cutting notches and stress risers

I'm reading about welding. Here's an article about how to cut a
'fishmouth' joint (and I visualize clamping the tube in a vice, in the
meanwhile making small marks in the metal), then the pre-cleaning
(using an abrasive, another thing my A&P told me not to use when
cleaning tubing) then the actually welding.

On the other hand, sometime ago someone mentioned the harm that might
occur if one were to mark on the metal with a pencil.

In one case you're handling the material and putting in a nominal
number of nicks and scratches; on the other hand I'm told not to mark
with a pencil?

What am I missing? - MIke