True, as far as I know, no CAD allows you to build with tolerances, maybe higher end software but I've not used them so I can't comment on them but frankly, neither does drawing by hand, in all cases, someone has to put tolerances on the 2D drawings that are sent to the shop for manufacture. You can build in clearance or interference fits but tolerances are why there are still engineers.
In Alibre, and I suspect other 3D CAD, you can in an assembly, insert a new part and to do that use existing surfaces, project to sketch which means pull 2D drawings from existing parts, draw your new part, change hole sizes and make offsets of existing components and dimension everything relative to existing components and then create the 3D part. Then, if at a later date, you change the parts the new one is relative to, your new part will change so it fits the new design. Yes, on paper you could do an overlay and trace your existing parts, this is just easier, more accurate and the design is updated when a change is made earlier in the design tree.
I still often use 2D CAD for simple parts, but more complex parts and assemblies are where 3D CAD shines.