When ever I have machined an Engine what was done was to mount the block on a fixture where the main bearing tunnel sat on a round machined straight bar, The block was then surfaced in situ on the mill that way the deck is parallel to the crank.

Next operation is to use an old school strap on boring bar which due to no vibration issues work far better than the fancy vertical mill type boring machines because the length of the head on those machines means they are not as accurate and you end up having to leave too much material so when it is honed there are no boring bar marks left.

We soon worked out those style boring machines are rubbish compared to a million year old strap on machine because the extra cost of stones worn out in the sunnen honing machine soon outweighed the ease of setting the block up and just running the block along with the table to bore the cylinders compared to unbolting the strap on and refitting it to do each cylinder one at a time.

Because the strap on fits onto the just machined block top face that is now square to the crank your cylinders are perfectly square to the crank when done that way, Followed up with a nice plateau hone job done with a torque plate and all is good.

It does make a noticable difference to making sure the piston heights are even (Well at least with quality aftermarket pistons)

So if machining a block those are the requirements for a really good base to build an engine from, If your local machinist does not have the gear to do it that way find somebody who does as the improvement in frictional losses will be well worth it.