Many of the things you mention, crossing out, circling, I do not think of as actively engaging with the material, which a quick skim of the underlying research pointed out in the TFA (or maybe an earlier 2017 paper of theirs) requires using the fine motor control of actually writing. Writing marginalia is good for the brain; if you disagree, write out why, if you agree, write your reaction. Highlighting, circling, crossing out are mere consumption and only useful for finding passages later, not engaging your brain.