Both common variables and permanent custom variables can be excluded from your document(s) when you don't need them. If you are using an "offer" type document then the excluded variables will appear at the bottom of the window when filling out the offer details and can be filled in for internal use only (this is optional and not mandatory).
Below, for example, the variables Bonus, Paid Time Off and Sick days were excluded from the offer document so you can either fill them out for internal reference or just ignore them.
Note: Deleting permanent custom variables which were already used it's not possible.