First of all, if you are using Altium 365, there is an assembly utility that is much more efficient then 3d PDF3D-PDF. It would solve your problem naturally by telling the technician where to place all fitted components. Therefore, your Tantalum capacitor would show or not.
Another way is to give your technician a free viewer license. That way, he will be able to interact with the tool and know which components are fitted or not.
If you prefer your current workflow, to export the 3d PDF3D-PDF with variants, you need to create an outjob file. These will manage how your output are generated. In the documents section, you can select 3d pdf3D-PDF. On the top of the page, there is an option for variants. By default it's at no variation. If you switch it to your variant, it should generate the right PDF. If it doesn't, report the bug to Altium.