You're one heck of a modeler if you can make real threaded parts match other threaded parts without interference. There's only one way (plus a tiny bit of tolerance) that a threaded nut will fit a threaded bolt, the start point of the thread must be exactly the same on both parts. If you have a bolted connection the nut will have to rotate to accomodate for varying thicknesses of the connection. So if you get it right for a few assemblies you use the same parts in, it will certainly be wrong for the other assemblies that use the same parts in other connections.
Except for cases where you really want to show the thread, and the number of threaded features is minimal, it is madness to have "real" bolts. It doesn't add anything usefull either. So cosmetic thread is the standard way you want to go. And when you do a global interference check you should first exclude all of the interior threaded parts/features, so that anything lighting up in the analysis is real interference : holes not aligning or having the wrong diameter to give clearance to the bolts.
Some people will model threaded holes to the nominal diameter instead of the pre-drill diameter to get rid of unwanted interference. This can of course be very dangerous if the model makes it to the shop floor without the info that it really is a threaded hole.
Alex
