There might be some confusion with terminology still. What section property are you defining with Z? It sounds like you're asking if the change in bending stiffness at the splice location will make a difference to the overall structure.
Estimating the stiffness of a connection is difficult, and likely not all that accurate. If this is what you are asking, I have asked myself the same question. The short answer is, of course the stiffness of the connection will make a difference - on the extreme end of things, if your end plate moment splice was closer to a pin connection, you'd have a hinge in your beam. If you have a well proportioned connection, I don't think it would make much of a difference. By this I mean, if your design only requires the splice to handle 10% of the beams bending capacity, I would design for something closer to 50-75%. I'm just throwing some numbers out here with my gut feel, if someone has any clear direction on this I'd love to see it.
The way I typically deal with this kind of uncertainty is to run a couple "sanity checks". In your model, at your splice location, insert a short member say 100mm long into your main member (or a node with a rotational spring)...and then you can play with the stiffness of your connection and see how it impacts the global behavior.