I have to go with the point on fitting the engine. Try putting those bolts thru the mounts when dropping a motor into a 70 Camaro or something like that with the front sheetmetal on and you are laying under the car with it on jack stands. You would be damn happy to have that little wriggle room and it would be perfectly clear why it HAD to be there. If it was a few thousands you would NEVER get that bolt in! There has to be a little room to make up for flaws in the location of the mounts on the frame and motor. There is no way there can be absolute perfection in where those mounts are mounted on every frame in every car, even from the factory. A little sagging of a frame over it's life, different brand mounts, etc, there are way too many variables to ever have a perfect hole for that bolt to go thru.
Use the larger, thicker washers and tighten it up well and there you go.