The risk is your pistons hitting your heads.

You'll read all kinds of opinions on this topic on the web. You'll find guys claiming they ran .028 quench, and never had an issue.

What is your method for measuring the deck height?

Machine shop method lol.

On the zero deck, I'd check it to make sure before you do anything. I've seen some engines that are supposed to be zero decked but are 10 out of the hole because they've been milled a few times after the original build. Always best to double check all your measurements before assembly. Such an easy thing to check and only takes a few minutes. Why not just put a bridge and dial indicator on it to make sure. There should be plenty of youtube video's out there too.

Looks like I'm going with Cometic .040 MLS on a gen 5 454 rebuild 8.25:1, 4.28" is it better to go with a 4.32" bore or a 4.375" bore on the MLS gasket?

4.320" is a better fit for that bore size.

I am using the Fel Pro MLS gaskets on cast iron heads / block combo. The finish was 70 RA according to shop. They are working fine, so what they say in the link is working for my setup at least.

Just be be sure to check and make sure the gasket doesnt protrude into the combustion chamber.

I use Hylomar(tm) if ya cant find that Copper Permatex #101MA will work just fine (Hylomar is a Rolls Royce approved product)

I thought I read on here the MLS gaskets don't require tack?