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Per the USPTO trademark database (on mobile so can't readily link), FiftyThree has a trademark on "Pencil by FiftyThree", not on "Pencil". Moreover the trademark they do have specifically disclaims exclusive rights to the word "pencil" by itself. (IANAL but typically USPTO will ask for these sorts of disclaimers if part of the trademark is deemed generic/descriptive.)

Similarly Apple's product is officially named "Apple Pencil".

So Apple is probably in the clear.

The exact same thing will happen that happened with Facebook Paper. 53 will write an angry blog post, get some free publicity, and then Apple will say they aren't changing anything.

I said it then and I will repeat it now, if you want to avoid name collision you shouldn't give your product a simple one word name that relates directly to your product.

It is not clear what question you are asking.

This is an existing stylus product that works with the iPad called Pencil.

It's not exactly an imaginative name for the direct analogue.