I'll preface this by clarifying that I'm not a machinist, but they do occasionally let me put down specs long enough to design machined parts. I also work in an industry where we often don't give a fuck about money.
But for a critical pinned joint like this, where even small amounts of play would not be acceptable, we would drill the hole intentionally undersize, and finish hone it until the actual bolt being used just fits. In face we sometime specify the allowable force to insert the bolt to make sure someone doesn't get crazy with a hammer because they are ready to go home.
Doing so allows us to get the fit we want regardless of the tolerance stack-up.