At the risk of alienating a few people, engineers aren't gods and even if they were, they aren't allowed by the Powers That Be (accountants) to build what they'd like.
There are lots of ways to improve the performance and fuel economy of a factory built engine and at the same time improve the life expectancy and reliability. Most of them were probably on the engine designer's wish list before the cost cutting for production.
GM offers crate engines that they can't put into cars that they sell. They know how to build better engines - and they're not alone.
I would have no more problems with my conscience decking a numbers matching block than I would boring it for .030" pistons, installing new guides, grinding the crank, line boring the block, sizing the rods, balancing the internals surfacing the heads, grinding the seats - all of which remove "original" metal that can't be put back - in the interest of building the engine to run the best that it can. I don't worry about duplicating some of the compromises that the factory made for the sake of saving a few pennies per car.
But that's just me. Everyone is allowed to do things their way! Now for a teaser: wouldn't taking .020" off the block with stock pistons be closer to factory than a set of custom pistons in an uncut block?