Hi,
we don't use Teamcenter, but we have used so I know how works with JT file. Anyway, we export for each NX parts the relative JT. For Assembly, we export in "MONOLITHIC" options. This solution create big file.
Exist the opportunity to export assembly to JT in the manner that when an user open the assembly JT file with JTtoGO, the software load components in a specific folder and relative subfolder like using the load options.def ?