Block out of square

Yup. I've dialed that back flange about 10 times, re-positioned the dial indicator mag mount on the crank flange each time at a variety of different angles. Each time, it reads out exactly the same. I also have mounted the mag base to the block and dialed the flange as the crank rotates. No runout at all there. So it's not a bent crank or a flange with wobble in it.
Very good that you checked all that. Makes it a lot clearer; tnx.

Wondered about that. There's a lot of open space around the edges of the flange, which seems counterintuitive from a cleanliness perspective... But at the same time, there's a 4x4" hole where the clutch throwout arm goes through, so... It's not like it's airtight to begin with. And the clutch is going to produce particulate as it rubs, so it needs a way to vent that out, right? Does having it sealed... even matter?
Depends on what you are doing... just a sunny day drag car? Not really. Driving in all weather? You'd like to keep the dust, dirt crud, and grease out. The standard bell are not airtight, but are reasonably well closed for all-weather use.

Yeah. Crate engine did the dyno test, we did not observe that test. But at the same time-- when they drop the block into the dyno itself, its not like they're mounting it using the bell flange. So, unless they're entirely disreputable... I don't yet have any particular reason to suspect that they'd have deliberately faked the dyno results.
Just wanted to know.... basically, I am not saying they faked anything. but you have no idea who did the dyno operation, and how well attuned they are to uneven running engines. The operator could have just run it through while day-dreaming about some hot chick.... So you just can't conclude it is either 10% or 100% OK inside the engine from the existence of the dyno sheet.

I like that idea. But If the crank is out of line.. Then... They'd have had to have re-decked the block to be square to the new line of the crank?
The guy that angled the decks on my block located the front-to-back alignment of the decking operation on the main web surfaces in the block, so the decks front-to-rear would follow any crank misalignment. So it is surely possible. And with the CNC setups that are out there, once one thing is off everything else would follow with limited intervention to catch issues. You want to know for sure right? And not just run it if there is any issue? Another thing to do is to do a cranking compression test as you suggested yourself.... you will surely have a change in back-to-front compression if the crank is out of square with the decks.

Okay, but... How big of a deal is that, really? I mean, if I have a taper in the back of the block that's 40 thou over roughly a foot, then over the .56" width of the head, I'm looking at 1.6 thou of variation from one side of the bolt to the other? Seems like I can just ignore that amount of error. I mean, do I trust my washer underneath the head of the bolt to be flat to less than 2 thou? Do I trust the cast bottom surface of the head of the bolt to be flat to less than 2 thou of tolerance? Do I trust the paint on the bell on both sides of the hole to be consistent to less than 2 thou of tolerance? Maybe I'm thinking about this the wrong way, but it seems like maybe that particular problem is ingnorable?
IMHO, the holes will only be off angle as much as the block's rear face, which is around 0.4 degrees; the contact gap on one side of the bolt head will only be around few thousandths of an " as you think. The bolts will **** a bit in the hole threading, and maybe bend a tad if need be and even brinnell the bell flange a bit. I personally would not fret over that.