F.e. crouch-use scroll on a waystone to bind.
To clear, craft the bound scroll in any crafting grid.
Using such scroll should forcibly activate the waystone upon successful teleport.

For this, I will probably add a seperate scroll type to keep the Return Scroll simple and seperated.

Well, that would be one more item to remember how to craft etc.
I though to keep it actually simple. Just use scroll on stone, write its name into NBT and tooltip. Craft it again to clear assignment, like many other mods, that use configurable items, do.

It's easier to craft another item (especially since people generally use JEI for recipes) than having to explain and understand two (very) different mechanics of a single item.

Making it a seperate item is the simplest form and self-explicable. Giving the Return Scroll two different functions would be unclear by default and only understood through experimentation, accidental clicks or external documentation.

This is why major mods include documentation in game.
Just ten words in the item tooltip could go a long way towards the gameplay experience.

It wouldn't just be ten words though when having to explain two seperate functionalities. The complicated tooltip in itself would already be proof that the item would be unnecessarily complex, while there is no downsides to a dedicated item for the new functionality.

That was unrelated to the present issue :)
I often find that a short reminder of the item's functionality saves a long trip to the google.
No need to explain everything in excruciating details.