If there's no wort left in the mash tun after draining you might as well set deadspace to zero. A few tablespoons probably gets left behind but not enough to worry about calculating into your water needs.
Pre-boil and post-boil is going to be different due to boil off. The wort pre-boil is less dense than post-boil so pre-boil gravity is always lower than post-boil. By boiling out 1.25 gallons of the 4.75 pre-boil volume you started with you're cutting out a quarter of the volume but keeping all the sugars so it's going to be a much more dense wort with a higher gravity.
I would make the correction on water volumes going forward and assume for this batch your post-boil volume was probably right around where it should be given the extra half gallon of wort you ended up with post-boil.