Apple Pencil (Generation 2): Will it overcharge if I keep it attached to my IPad Pro?

No it’s designed to be kept on the iPad. It will stop charging at 100% then maintain between 95 and 100% battery.

The second generation Apple Pencil should be kept docked with the iPad when not in use - as this ensures that the tiny internal battery is kept healthily charged when not in use. 

Keeping the Pencil is a separated when unused risks allowing its battery to discharge; if allowed to remain in this state, the battery will suffer irreparable damage. When the battery fails, the only remedy is to replace the entire Pencil; the battery is not a serviceable item.

It is perfectly safe to keep your Apple Pencil magnetized to the side of your iPad Pro. It is designed to be a safe place to keep it where it won't get lost and will always be ready to be used when you need it.