Yes, set focus will correct for the additional thickness. The chipboard or whatever paper product the cover is, the smaller and bigger are probably identical composition. Once your tests result in a depth you like it should replicate fine.
The spiral binding isn’t a problem as long as it doesn’t exceed the 1/2" focus limit with the tray in. With the machine off, you can put the book in, open the front door and look under the gantry while you move the head over the notebook to be sure it clears the air assist fan duct on the bottom of the head carriage.
If the spiral wire is greater than 1/2" you can remove the tray and shim up the book. This is handy to be sure your work is within the focus range.