Not directly, although you may be able to replace the entry point (signtool.exe in our InstallShield\system folder) with an exe that reinterprets the command line parameters to use the certificate store instead.
Our company believes that the certificate store is more secure and you can control the exportation of the credentials. You should really consider adding the feature instead of force installshield users to overwrite this exe. I think that'll make support issues more complicated when you send out an update.
Agreed; replacing that EXE is inelegant at best. (Although the odds of us replacing that file are really low, so it's more a concern that when you upgrade to a new major version, or install on a new machine, it won't sign correctly.)
