I found a post from a couple of years ago where you recommended a couple of apps for this. I’m thinking of Laying Down the Rails for Children (trying to decide whether to go paper or ebook) – for “writing” in the book. Would either of the apps you mentioned (iAnnotate and I can’t recall the name of the other right now) work equally well for this?
It is allowed by default but a publisher can choose to restrict it. If it’s one of our books then there will be no restrictions because we just treat you as we would want to be treated and trust you to do the right thing with the materials. However, some publishers may turn on every restriction possible out of fear and not realize it’s an inconvenience to you.
What you want to look for is commenting or annotation features in whatever software you are using. However, if a publisher disables commenting then your annotation tool icons will be dimmed so you can’t use them.