This guide is a part of a series of 3D asset creating process related wiki sites 3D Asset Workflow
For modeling you'll probably find a lot of useful general info on the Modo guide

Preparation

This guide goes into detail on how to bake billboards using Substance Designer
Export your game-/editor-ready low poly mesh as their own fbx-file
You can have multiple meshes in a single file as long as they use the same texture maps and they are named properly
Same way as if you were baking with Substance Painter
See Baking with Substance Painter for reference
You will also need the diffuse/albedo, normal map and specular map for the exported low poly

Create your billboard mesh

Import your low poly mesh into Modo
Go into front orthographic view by pressing numpad + 2 (revert to perspective with numpad + ,)
Use the pen tool to draw a plane that covers the low poly mesh. Try to make the plane silhouette match the low poly as closely as possible to reduce the number of rendered transparent pixels.
Connect the vertices (Ctrl + L when 2 vertices selected) and create a UV map
Center the billboard and duplicate it to a new mesh layer
Move the duplicate away from the low poly, until they no longer intersect
Now you have 3 meshes: Game ready low poly (used as high poly), billboard plane (used as low poly), and the offset duplicate (cage)
Export your billboard and cage as separate files

Open Substance Designer and make a new substance (File > New Substance, or Ctrl+N)
- Settings don't matter at this point, empty graph works as well as any other
Right click on Unsaved package in the left side panel, and select Link > 3D mesh
Select your billboard mesh
The imported mesh can be found in the resources folder in the same panel
Right click on the imported mesh and select Bake model information

In the dialog, click on the small + -sign in the middle panel labeled 'Bakers', and select Transferred texture from mesh
Add 3 of them. Select each new entry and point them to albedo, normal and specular.
Remember to tick Normal map -checkbox in the case of normal map
Reference for Substance Designer bake settings:

Most of these settings are the same as in Painter
In the right side panel, select the export folder, output size and dilation amount and/or diffusion
For the high definition mesh(es) select the game ready low poly
Add the cage if you have one. If not, increase the Max Frontal and Rear distance until no clipping occurs.
Match By mesh name if you are baking multiple meshes at once and have them properly named. Otherwise use Always. Antialiasing 4x4 or 8x8.
Press OK to bake the maps

For a opacity map, that has individual leafs and their back faces taken to account as well, start by importing your low poly tree into Zbrush
In Zbrush Separate your leaf planes in to another subtool
You can do this by using Auto Groups in polygroups menu, then hide all the leafs and in subtool menu -> split hidden.
Now Import your opacity map for the leaf planes into Zbrush
Remember to flip your texture in ZBrush. Texture -> flip v and apply it to the leaf planes subtool
For applying the texture into your leaf planes go to Tool -> Texture map
Applied texture on leaf planes:

Next you will need to subdivide the leaf planes in such way that they don't get smoothed
In Tools -> Geometry next to Divide button turn Smt off
Subdivide the mesh until it is over 1 milj points
You might need even more subdivision if you are not getting desired sharpness/resolution later
Transfer the texture map in to polypaint: Tool -> Polypaint -> Polypaint From Texture
If the Polypaint looks blurry try increasing the subdivision and repeat Polypaint From Texture command

Next you will need to polygroup your black colored areas and delete them: Tool -> polygroups -From Polypaint
Now to get backsides to show up for the leafs apply panel loops to them: Geometry -> Geometry -> Panel Loops
Adjust the thickness to be low amount and set Polish to 0
Also you can decrease Loops amount. Test what thickness value works best for your asset.
Thickness value is effected by the assets size, so it can vary with each model
Merge your leaf plane subtool into your trees trunk and export the subtool out as obj or FBX
How the tree looks like before exporting it:

Create low poly billboard planes for your tree and cage mesh for it as well
After that in xNormal set the model that you just made in Zbrush in to the high poly mesh slot
And add the low poly billboard model in to the low poly slot. By right clicking in that same slot you can assign custom cage mesh.
In Baking options select for example Bake base texture as the map you want to bake
Set Edge padding to 0 and antialising to 4x
Once the bake is finished open the map in Photoshop and turn the base color to white or copy that textures alpha channel, as xNormal creates for all of its bakes usually an alpha channel also.

The baking process is the same, but instead of Transferred texture from mesh, select Opacity Mask from Mesh From the bakers-panel, and change the high definition mesh to the one described above.

In Photoshop, paste the baked opacity map to the textures alpha channel (Add the alpha channel from the channels tab by clicking on the new channel button).
Only the albedo needs the alpha channel, so save it as a 32-bit tga and name it [texturename]_alphatest.tga.
Export the rest of the maps as 24-bit tga and name them [texturename]_alphatest_[suffix].tga.
More about naming conventions in Naming conventions.
After importing the billboards to the editor, check BillboardY in the model component to make the billboard follow the camera on Y-axis.
On the left is the billboard version of the fern group seen on the right: