When I design parts that must fit in each other, I usually keep in mind that prints are 0.2-0.5 mm wider than expected (depending on material) and I size the parts accordingly.
However, sometimes I design the whole part and then I slice it with planes or lines. In these cases I need to push/pull afterwards each contact surface manually by the same amount (0.2-0.5 mm) and that is a time consuming task. Another option is to use a cutter to remove the outer surface layer (basically I remove the rigged surface, making it smooth again) but it's not safe and even more time consuming.
How can I quickly generate said controlled gaps on the contact surfaces between two objects, but not on the rest of the object? to make it everywhere I could use shells, I guess, but I don't need that on the whole object.
Unfortunately, 123D Design doesn't have such a feature.
You could select multiple surfaces and push/pull them all at the same time though.
Remember, your 3D Printer's slicer should have an option to undersize or oversize holes and walls, to help reduce/remove the effect you talk about. It's called size correction, I think? Simplify3D Has it, atleast. You might have to tweak this for every filament type, though.