You can swap back and forth between VFR and IFR several times. I think Y means you depart IFR planning to switch to VFR (and possibly back and forth several times), Z means you departed VFR and are going to switch to IFR(possibly having switched back and forth several times).
leaving a German VFR only field and then arriving in Lido (Italian VFR arrival required) with an IFR enroute seems to need to be filed as Z (and CFMU doesn't choke on this).