Software Endstop Issue

i am really excited about this feature here are some things that i
notice.
because i have software endstops enabled then i cant go more negitive
than where the Z endstop hits.
i want to leave software endstops enabled for safety of the printer.
but while this routine is running i dont see a problem with letting it
go say 5-10 mm below the bottom software endstop so that i can select
the correct z offset.

Also right now if you do happen to hit that bottom z software endstop
then the height wont get decremented but if you try and go up then it
will get incremented. and so if you go back and forth, the actual height
of the print head wont move but the software ZOffset will get big. This
seems to be resolved by allowing the printer to go outside the box by
5mm. it will probably still happen but i would run into the bed before i
got there.