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Your Gears should be modeled to nominal [BASIC] values.
Tolerancing must be thought thru at a system level to afford F,F,F at the assembly.
Gear mess tolerances should follow industry standards.
Your gear mesh should be adjustable at the assembly; typically by slotting one of the Gear's axis.
I must assume that if your gear profiles were created at nominal values then you should be safe to go ahead and 3D print these. I all will depend on your application, Size of gear, # of teeth, type of 3D printer, print resolution, etc, etc.
But the question of tolerancing in 3D in 3D is somewhat misplaced... your 3D is a theoretical perfect part. Tolerancing is only to account for manufacturing variation and the fact that the "real world" is not perfect.
I hope this answer is helpful... if I have misunderstood your question please elaborate...
Found a link to machinist handbook GEARS, SPLINES, AND CAMS chapter via a .edu site...
this either could be done using the Thicken function (at least for positive tolerances, I'm not confident about negative yet) or using an Offset Surface followed by a Replace Face function.
This will work in both directions.
Those methods will give You the possibility for modifying the tooth geometry with appropriate tolerances according to Your wanted functionality!