This is something I've discovered while making my Modloader work to start mods via Steam. Perhaps it can be useful. It will start it through Steam from a .bat file only if Steam is installed.
The pro is that you don't need to define where Steam is located. Con is that Steam will warn you before starting it that it wants to start Amnesia with X parameters.
Moving on:
Try running something like this in CMD.
start steam://rungameid/57300//mods%2Fmodding_mod%2Fconfig%2Fmain_init.cfg
start executes the following.
steam:// is a protocol recognized by Steam when installed.
rungameid tells Steam to start a game. 57300 is the Steam ID for Amnesia.
This will act as running Amnesia with "mods/modding_mod/config/main_init.cfg" as the Steam launch option. Keep in mind that this uses the steam:// protocol which is URI formatted. This means you must use %2F as replacement for / and %20 as a space (if your path uses spaces). There's more but these are the most important.
After running this command, Steam will give this warning which must be accepted in order to start it:
You can incorporate this into a .bat file for retail and a .bat file for Steam. I'm sure it's possible to put them both into the same .bat file in some way.
Edit: I'm getting some odd results from a .bat file where it ignores "%2" from the line, likely due to CMD using these as variables. Anyone know how to avoid this? It works fine if you paste it into CMD, but .bat acts differently.
Edit 2: Found out. Apparently you must use
double % signs to escape this functionality. Basically this means the above only works in CMD and to run it in a .bat file (which is the goal), use the following instead:
start steam://rungameid/57300//mods%%2Fmodding_mod%%2Fconfig%%2Fmain_init.cfg
So essentially what you must run is "start steam://rungameid/57300//" + your main_init.cfg path edited to use %%2F for every folder level and %%20 for any spaces.
Whew, such a pain. Hope this helps though. If anything, it's useful information.
Here's your specific line. Save it in a .bat and try.
start steam://rungameid/57300//TRIAD%%2FTriad_config%%2Fmain_init.cfg