The rules say about the attacker measuring the distance from centre to centre of attacker and defender's base to determine which section can be targeted. Does this same rule apply to the actual range determination or does that still get measured from nearest point of each base as per the standard rules?

Still nearest point to nearest point

You determine whether it's a legal shot by measuring post to post (to see if it crosses the blue line / C-ROC arc line or not). If it is legal, then you measure from closest point of that half of the epic ship to closest point of the small/large.