Advice please.

I charge shipping on most of my listings, quite often using the Australia Post calculator. I sold a board game over the weekend where the calculated postage was $18.95. It wouldn't fit in a large satchel so I just double wrapped it in brown paper to post. I was only charged $14.95.  I will no doubt give the buyer a $4 refund out of good faith but was wondering what others would do in this situation. 

Is it best to include shipping in the total cost with free shipping or have the shipping separately ? Any breakable/easily damaged items I have sold, I have gone a little overboard with bubble wrap & don't charge for that.