I forget to ask, how do I use Tcl to set the Set Application form?
The control is mostly cosmetic, in the sense that you can still [issue the command to] start a run, even if a check is grayed out. So if your batch script does an ERC run, whether it's gray or not is only for the convenience of the user looking at the GUI. It might seem this would limit the electrical checks you can do, but in fact, it's only there to guide a circuit designer using the GUI, while all ERC option settings are still possible. Another thing this control does is to show or hide device parameters that are optional. For example, a MOSFET gate capacitance is not required if the user hasn't set a custom digital workflow with drive-vs-load / fanout preference. So analog designers won't bother with fanout requirements.
OK, so to update those workflow settings, use the command:
project application _type_ _checks_
where _type_ is either -digital | -analog
and _checks_ are -voltage -floating -fanout -keepers -others
plugin refreshLibrary -filtered
That will update the GUI.