I've found a solution

Fuck it, I’ll write in the margins.

I can write in the margins now using a colored ink. If I decide to scan my books later, I can filter out the color and the digital page would be clean.

Pros:

• I (or whomever inherits the book) can read my notes later
• I can make secondary annotations in a different color

Cons:

• I can’t search my notes (or the book’s text)
• Focus is lost from the text when reading through a second time