Hello,
Publishing to a Substance 3D asset file (SBSAR) includes Substance graphs and their dependencies exclusively. If the outputs of a Substance graph are used in an MDL graph, these outputs are baked as static bitmaps into the MDL file.
If I may ask, to what end do you need to use Substance 3D asset files as MDL files?
If you require the procedural behaviour of Substance 3D asset files for generating textures in another software, then you may download the Substance 3D plugin for this software – if one exists – so it supports Substance 3D assets file which you may then feed to your MDL within that software.
The MDL and Substance 3D asset file need to be imported and managed separately.
Since Substance 3D asset files are archives, you may open them using an archive utility such as 7Zip and package MDL files into them for easier distribution. Additionally, you may add metadata in the SBS package which points to the location of MDL files on the system by selecting the package in the Explorer panel and adding metadata entries in the Properties panel.