Well, here's the final word from Mercruiser. Their initial response to my question was this:<br /><br />
Thank you for your recent inquiry. The sterndrive and transom assembly do not change regardless of the model of the engine. The setup on the transom side is either for an Alpha assembly or a Bravo assembly. The "Y" pipe setup needs to be the approved exhaust application to work with your 5.7L and Bravo sterndrive. I cannot authorize the use of only three bolts when four bolts was the original planned design. MerCruiser recommends making any necessary changes to insure that both top bolts do line up and attach accordingly. I hope this information is helpful and please let MerCruiser Consumer Service know if we can be of further assistance.
After writng back with a reminder that my boat doesn't have a Bravo drive, but an Alpha one, (as I had originally said!), I received the following response back:<br /><br />
I spoke to a technical expert in the MerCruiser OEM department about how that should bolt up. He said that on some applications that you will only be able to access three holes to complete the assembly. It is completely normal and an approved method. That is officially MerCruiser stance. Sorry for any confusion.<br />
So there you have it - straight from Mercruiser. I guess it's okay to only use the three bolts for the "y" pipe after all!