I've wondered about this in the past. Even drilled a set of gaskets once to match the block. Seemed to work okay, but I can't suggest it. Last couple of times I've had mine off I've just installed them accepting the pattern and have found that it actually it stays cooler, and here's (I think) why: you want the water to run front to back through the block, then return through the head, utilizing the large passages at the front & back. I believe this keeps coolant moving all the way to the back, and keeps the water flowing in a pattern. If the coolant was allowed to flow down through the gasket too much, you'd get hot-spots as it wouldn't flow all the way to the back. At least this is what seems to make sense to me.

Basically, install them and ignore the desire to see the gasket passages align with the block & head passages. It works, don't sweat it.