1) As far as I'm aware, it is one 3D model per decal. You can create a composite model (i.e. combine the TO-220 with the screw & nut into one 3D file) or simply import the screw & nut separate from the part and align them manually but there is a 1-to-1 model-to-part relationship.
2) The model is related to the top of the decal - you can flip the model but then you will have to manually adjust the Z-distance based on stackup thickness. It would probably be easier to push the decal to the bottom side.
3) At this time, there are no through pin holes - I expect that we are working on this.
4) The main advantages of M3DL are:
- Library searching - you can find models based on parametric queries (e.g. find 3D models with more than 22 pins, find red LED's, find models associated with Atmel, etc.) You don't have to manually search through a huge directory of STEP files.
- Faster setup - you don't need to create the models & align them to a footprint. The M3DL models have pin information and will align automatically. Many customers don't have a dedicated mechanical team creating 3D models for them - this gets them several thousand models right off the bat.
- Embedded intelligence - the models contain information on material properties (i.e. made of glass, metal plastic), through hole pin size, underside height, and other items. This can come useful in other analyses - for example, they have an associated mass so you can use them to do vibration & shake analysis on the board to see if it yields after a certain number of stress cycles.
5) Some short answers:
- Part holes: the 3D export will probably cover part holes once they become available in the 3D view.
- Copper: export already handles traces, vias, and plane data - you can toggle whether these are exported or not by enabling/disabling their visibility in Display Control before exporting. I am able to generate a 3D PDF of the board with copper & without copper this way. I have not tested STEP yet but expect it functions the same way.
- 2.5D models: export will use those if no 3D model is available. If a 3D model is assigned, it will use that instead. There is no option to toggle between the two - once you assign a specific model that should supersede the generic "estimate" based on component outline and height.