Are you thinking about a certain setting in the Configuration Parameters which may be in conflict?
It is certain that both need to have the same System Target file, also the 'Device Vendor' under 'Hardware Implementation' need to be the same. Just to name a few.
I work with reference configuration parameter files inside a shared data dictionary to make sure my top model and reference model have the exact same configuration parameters. This way, I also switch between configuration parameters for for example embedded code generation, real-time prototyping and simulation. Each have their own different configuration parameter set.
