My guess on the instruction booklet is that when you come to the final sanding, it is likely that you may sand close to the glass in spots and therefore require a skim coat before fine sanding and varnishing. As for between coats overall, if you apply subsequent coats within the time frame (chemical bond), sanding should not be required nor recommended as you may dullen the soft epoxy by rubbing in fine dust. Quite often in practice though, if coats are not even, it may be better to let the last coat harden and then scrape down runs, sags, etc, and then apply the next coat (mechanical bond) to the smoother surface. However you apply (chemical or mechanical), in the end, you want as mooth a surface as you can produce to reduce the effort in sanding the very hard epoxy for varnish.