Given that it's a change of behavior, I would also put the blurb about when using --upsertFields, you don't need --upsert in the upsertFields section as well.
Basically, if you're an existing user, you might not read the --upsert flag section (although, visually, it's just above, but one never knows how what's displayed on screen).

Also, I'd tweak the wording a bit. So currently we state:

Changed in version 3.0.0: --upsert is no longer needed when specifying upserts. Use --upsertFields, which produces the same behavior.

But, if I take the first sentence on its own, it's not quite true. You don't need --upsert if you're not using --upsertFields. But, if I'm fine using _id field as the field to check for existence and so I don't explicitly state the --upsertFields, the --upsert should be fine. Steering people to prefer --upsertFields is fine, so if you want to go with something like (the following is just blurbage, so feel free to edit or change wholesale at will)

Using --upsertFields now implies --upsert, as such, you may prefer to use --upsertFields instead of --upsert.