When I get a block back the bock saddles are barely touched. They have marks, but the centerline is NOT moved. If yours is deeply honed in the saddles then yes, your shop more than likely moved your centerline a small amount and it wasn't done well.
66fs - It's my opinion that you cannot square deck without properly locating the crank centerline. I think your belief is the bore can be located anywhere in 3d space and so long as you index off it that means the decks are square. I would agree if that the centerline could be "anywhere" if we were only concerning ourselves with the engine. However the location and direction of that centerline also affects the driveline "downstream". Power to the wheels is lost when things aren't lined up perfectly. Align boring/honing corrects the accuracy, position, and angle of the crank to exactly perpendicular to the bellhousing. Square decking takes that a step further and makes sure the decks are parallel to the crank centerline and perpendicular to the bore centerline. If you don't correct those relationships you didn't "square deck".
If someone thinks factory is "good enough" I'd suggest using the deviation from deck height specification as a gage of accuracy of factory machining. I don't know of a single Mopar block that's not taller than the blue print height. Some are tall by a hundred thou from there. The same worn mass production equipment did the crank bore, the bellhousing holes, positioned the cylinder bores and drilled them.
I strive for a result that is much bettter than production line quality. If you want a 375hp 440 then factory's fine. If you want a 500hp 440 it becomes more important. If you want a 550hp 512 it's even more so.