The closest spot is the top of the piston, inside... like closest to the valley. This is also where the squish area is. It's perpendicular to the pin axis, closest to the valley (the lifter area) on the block. piston to wall clearance, bore size, and overall piston height are what affects the amount it rocks at TDC. The shorter the piston, the bigger the bore, or the wider the piston to wall, the more rock at TDC, and the closer the piston will come.
The reason I do align honing is the fixture that allows for a square deck indexes off the cam and crank centerlines. Align honing allows the crank centerline to be perfectly aligned in the block, which in turn means the square decking is that much more precise. The difference between decking, and proper square decking, is about $100K worth of machining center. Decking is simply taking material off the head gasket or deck surface. It's an "as good as you can do" type of thing because the block is leveled by eye (with a machinist's level) to the table, rather than the deck surface indexed off the crank centerline. A shop can buy the setup to square deck with an older horizontal miller. But at best, assuming no slop in the arm or cutter head and no error in the eyball or the level, the cutting head will still be a problem because of the path the cutters have to trace going on the disc they mount to. You cannot get the deck surface perfectly flat because the center of the arc the cutter traces will always be a deeper cut than the sides. A modern block machining center has a single cutter that can reduce that accross-the-deck depth difference to under .0005". Usually, you can take a "decked" block, put it in a square decking fixture, and take measurements off various points and you'll find variences of as much as .015-.020" from end to end and somtimes more on the diagonal. It's no wonder there are issues in some engines with pushrod length and preload, noisey lifters, deontaion and ping, when others are fine... All that is affected by the geometry of the deck surface. Nevermind longevity, power, and smoothness.
