I don't own a Note 5 and have no plans to get one, but I don't see this as a problem I would have.
I put this in the non-issue category.
It's about as much of a design flaw as every shirt on the planet, which can be put on inside-out if you aren't paying attention and then getting permanent deodorant streaks as a result.
Can you design a T shirt that is physically impossible to put on inside out? No (well, maybe--then you'll be onto something ). But you can with the S-Pen--Samsung did it with the previous generation of the Note and thus, we never heard of this problem. They choose to not integrate that restriction into their current S-Pen and now they have to deal with this admittedly stupid issue. Could've avoided the whole thing with a better design.