Usually on most engines(general) there is a measure spot on the block you measure from to get this number from. Same with heads there is a mark to the head surface you can measure so you know if its been cut or not.
Where that is on ours is a good question for for an engine shop if your lucky they work on Hondas.
I think on American V8 they use the crank center line as there datum and move out but thats just a guess on my part.
EDIT: guess backed up by a link
CNC Engine Block Maching:MA,CT,RI,VT,NH,ME,NY,NJ
"blue printing" and engine block would be a good google search start.
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