Lets say I import a bolt STL and use that bolt to subtract from a body to make mating threads. However naturally the bolt would be near impossible to be screwed into the threads because of tolerances. Is there a practical way to create a tolerance in this kind of situation? Scaling in one dimension comes to mind as an easy fix. Hobbyist asking 
Interesting vid on the subject.
Yeah, but the amount of scale really depends on the chosen technology for manufacturing. Please note that scaling a bolt’s cross section would result in an ellipsoid cross-section, in this case at least two dimensions are needed 
From STL I guess you are thinking about 3d printing. Once I designed an M45 thread and had to use 0.25 mm offset surface on each side to make it usable after printed on an FDM printer with d0.4 mm nozzle. SLA would be much better, but this whole title is the field of trial and error 
One might also want to ensure their 3D printer is calibrated. Don’t assume the factory got it right and check it regularly. Like any tool it can require a tune up.
For threads what widly used is “COARSE” I think.
Tolerance for other things means different things.
For stainless steal for example it means calculated expansion of the object after making
For other stuff means different things
Sorry auto correction 
Most of what I do is 3D printing, Yeah I meant 2 dimensions. Oval bolts might look cool but no fun to wrench on.