If you can get NCM to successfully backup a config, then you'll be able to get it to compare running/startup configs. Depending on the device you'll need to play around with the Login Information and Communications sections for the device. For some device you may need to create a Device Command Template or do a search as someone may have created one already.
For example, I backup the configs on some Tandberg devices I have.For Login Information I have the username and password and Enable Level set to <No Enable Login>. In the Communication section I have a Tandberg template and Execute Scripts Using, Request Configs Using and Transfer Configs Using are all set to SSH2.
If you can connect to a device and download a config somehow, then NCM should be able to do the same thing.