As KarlIT and J1D mentioned, preload is necessary to keep gripping. If the load is alternating like wind on tower, without preload, the joint become loose or gap between base plate and foundation will form. In that regard, I think the preload should be near design bolt load. On the other hand, as chichuck hinted, concrete around top portion of embeded thread may be damaged. That concern would limit amount of preload. This is simply my thinking, though.
Any way, as for the reason why preload affects baseplate thickness, the bigger preload is, the more bending at off-bolt area will occur. Even though addition of load(wind) will reduce bolt tension and thereby reduce the bending contributed by bolt tension, because bending contributed by load(wind) will always overweigh the decrease, net amount of bending with bigger preload is bigger than net amount of bending with smaller preload. Bigger bending requires, of course, thicker plate.
But I am not saying that preload should be considered when calculating baseplate thickness. If many engineers designed baseplate without considering preload, I think, there must be good reason.
My assumed reason is : Usually the most-bent area in base plate is outer edge of the plate between bolts, whereas bolt preload affects this area very liitle. It seems to me that bolt preload affects mainly only the area near bolts.
Any comments will be welcomed.