When fitted correctly you should see a tiny gap, of about the thickness of a sheet of paper, between the tip and pencil body. If slightly loosened, or overtightened, the Pencil may not work properly. The expected gap does not appear to be evident in the first image for the upper Pencil.
Unless unavailable, when the Pencil tip requires replacement due to wear, you would be best advised to replace a tip with Apple replacement parts - as these will be manufactured to Apple's high quality standards and engineering tolerances - and will be using the correct polymer materials. When using third-party replacements, you don't have this assurance.
As for your "alignment" issue, consider that the Pencil tip does not actually attach to the main Pencil body, but is screwed onto the transducer assembly - allowing the Pencil tip to move (albeit minutely) independently of the Pencil body. Inevitably, this may lead to tiny variations in alignment between the Pencil body and tip.
If you are using a genuine Pencil tip - and you believe that misalignment between the two components is excessive or incorrect, you might try swapping the tip for another genuine item. Otherwise, you would be best advised to return a new Pencil to your retailer for exchange.
Alternatively, a visit to the Genius Bar at your local Apple Store will provide opportunity for your Pencil to be assessed by Apple Technicians - and explore your available options.
