Uneven fit like that happens when the briar block shifts a bit in the chuck between the mortise drilling and squaring the shank end, leaving the mortice and the shank end not quite perpendicular. Happens a lot.
Sorry, but no. High volume production pipes' mortises are drilled with a type of bit that cuts the end of the shank simultaneously.
Briar changes shape with use from temp cycling, moisture cycling, and pressure. If it changes enough, permanent (meaning when at room temp and dry/not recently smoked) misalignments appear.
Minimizing the problem and reversing misalignments after they've appeared are best discussed separately.
As to the OP question of whether to be concerned, not structurally, no. It can be set right if it bugs you, though.