I had to have one of the heads on my last build angle milled to make up for a bad previous decking the block had received. After a lot of measuring and checking, I determined that, although the deck was flat, it was .030" lower in the back than the front. I finally found a machinist who understood my problem and was able to mill the head a compensating amount. Decking the block was not an option because the short block was already assembled and the notorious thinness of flathead decks. If there is any interest, here's a link to a thread about it :
https://www.fordbarn.com/forum/showthread.php?t=228269. Beware, it is three pages long and there were some disagreements.
While this may not be the case in your particular situation, it did end up with me having a head milled more on one end than on the othere, so it CAN happen.