In terms of ignoring books in Goodreads, I would think you have two options.
The first is to put them on a custom shelf that you don't ever sync with.
The second is to just not link them. When you sync with a shelf, the plugin will only sync books you have linked. When you click on the sync button with some of the books on your shelf not yet linked (like your DTB books) you will get a warning popup, but it is just that, just a warning. You can go ahead and perform the sync and your actions will get applied to all the other (linked) books for that Goodreads shelf.