To my (limited) knowledge it is possible to start Thunderbird with a batch script where you can specify which profile it should open. These profiles must exist, you cannot create these on the fly.
skwire is also right, applications need command-line support before you can use them in a batch script. Never, ever expect this support and even if your application has command-line support, don't expect too much usable options/parameters to be included. Besides, the use of batch is dwindling and there is some push towards PowerShell for the persons that make use of the command-line. With good reason, PowerShell is much more powerful and allows you to access applications in ways batch scripts cannot even dream of.
There is nice freeware (Idera
) around that enables you to make scripts yourself. It comes with auto-complete, descriptions of all commands and their parameters + working example scripts, a debugger and access to community where you can download scripts as well.
Whatever time you dedicate to PowerShell with this software, it will be time well spent.