Based on a comment by @Praetorian, I opened the model in a text editor and found the parameter line where the variant condition was defined.
I found that the variant conditions are stored in the subsystems within the variant subsystem and not within the top-level variant subsystem.
So you store the condition within each subsystem's "VariantControl" parameter.
Example:
set_param([variantSys '/' sys],'VariantControl','a==1')
where sys
is a subsystem within the variant subsystem variantSys
.