Not sure if vertex animation works properly in Source 2 (importing ones exported to DMX seems to be broken at least). Unless you can get that working, the only option available seems to be to skin each piece of glass to a separate bone and bake a skeletal animation from the physics.

Not really, I'm not even sure how they work. I think they're already supported for Source 1, but IIRC I tried settingthem up once and Source 2 didn't like them.

The whole system is confusing, and I haven't been able to find any documentation on it.

I'm not sure if driver based shape keys work.

I made an experimental modified version of the tools that can can export directly keyframed shape keys to a Souce 2 animation DMX. Currently it will export all shape keys in the file for the duration of the skeletal animation in the action, so make sure you have some bones keyframed.

No guarantees it won't destroy your files, so make sure you have backups before using.

https://github.com/Rectus/BlenderSourceTools

I did a quick hack that just rotates all bone transforms 90 degrees by the Z axis in the DMX export, and it makes life so much easier.

I have my experimental branch of BST here: https://github.com/Rectus/BlenderSourceTools (use with caution and remember to backup your work, I haven't tested all the features, so no guarantees it won't mess up your models)

I've mostly made props, but testing with a quatripedal character at the moment.

Not sure about finger rolls, but Source 2 seems to generally use the X forward, Z up convension. Ragdoll joints can only be configured to rotate on the Y and Z axes (no roll), IK chains require the X axis to point at the next bone in the chain, and the old model editor expected the Z axis to be the surface normal for cloth when generating cloth nodes of the skeleton. The AminGraph movement system considers the X axis to be forward on the model as well.

Reagrding the scale, I want to be able to reuse my assets in other places, and getting an accurate scale can be important when working with VR.

I was thinking of a simple multiplier, so you can fill in any scale you want. These are pretty standard features for most model exporters, both of them are already supported by things like the Blender FBX exporter.

Not sure I'm following you here. I don't see the point of having to do those actions manually every time I export a mesh or animation and then revert the changes, when a script can do it automatically.

Source 2 seems to expect that the X axis of a bone points forward to the tail, the Y axis to the side and the Z axis up. This makes connected bones exported from blender break several features, like ragdoll joints, IK chains and cloth nodes.

It would be very useful to have an option to rotate the bone axes on export.

Also, a feature to set the scale of the exported model would be greatly appreciated. I like modeling things in metric, so I've taken to scale up the model by 39 every time I export and then scaling it back, but that gets tedious.

I found another color attribute, this one is simply called color$0. It is what gets used by the SteamVR tools to set vertex color tinting when Vertex Color is enabled in the material settings.

Sure, although the official model probably shows it better.
https://drive.google.com/open?id=1LNy7OFBlvopoYzmkTGnvbtMXlD3TDI-z

Unless I'm setting it up wrong, that seems to generate additional morph channels and drive those using a joint.

The kobold model above drives the morph channels directly with a DmeChannel with float values using the flexWeight attribute instead of position.

I managed to make and export an animation using this method from SFM, and I think Valve animated that kobold model using SFM as well:
https://twitter.com/rectus_sa/status/1223578875982073856