The models should always reflect the finished product. You should not have to "fudge" the drawing if the parts are at the correct sizes.
As Troy said, the model should reflect the actual part. Dimension the hole to give you the desired amount of clearance. If you have a Ø1" shaft and want a Ø1.005 hole, then enter that dimension. The display will probably still show 1", depending on your settings. When you get to your drawing you may need to change the settings for that dimension so it will show correctly.
You can put your dimension tolerancing scheme into the dimensions in your model
and insert them on to the drawing using insert model items.
You can also further your design intent by using the dimxpert and add dimensioning intent
along with GD & T to your models as well.
With this intent built into your model there should be no reason to fudge anything.
Thanks to you all for clearing that up for me.
Does it really matter? Bore and shaft each have a tolerance range. There are different reasons one might have for modelling at either end of that range. As far as mating goes, concentric mates work regardless of diameter.
I work with for a company that does design for many different clients on various CAD software.
We model everything line to line.
Within SW you can set the tolerance in the model and have that carry through into the Drawing.
With CAD systems there are many ways to get to what amounts to basically the same result. The method you choose to use will depend on your required results coupled with the ability and methods used by the shop producing the parts you design
Just another option represented.