The scripting in designer is pretty half hearted at the moment - it'll get better with time though. Looks like you're on designer v5 from the path in your OP so you have no designer scripting nor access to the automation toolkit. Your best bet is to knock up a little python library to construct command lines and launch it…
I decided to do some experimenting with the Substance Maya Toolset Mel script written by @Froyok and I've run into a problem I can't think of an easy solution for. When I try to run the template baking it won't generate any of the inputs. The error I get is this: Found no parameters in "test.sbsar" So I opened the script…
The way this is supposed to work is that you're sending a command line to the various .exe's and there's some discrepancy between how strings are represented in mel and the windows shell. But you're right - I'm thinking the best thing would be to just ignore this and rewrite some similar tools in python inside substance…
If it's any help, this stuff works fine from standalone python and c#. I don't do Mel, does it handle processes sensibly or are you forced to just send a massive string to windows and hope? (maybe put some extra quotes round it)