John Sigismund would naturally keep his rights on Transylvania only and would be heir of Ferdinand in Poland only if he had no half-brother... Ferdinand jr not Isabella would be King of Poland in this scenario... Still Isabella would secure at least TransyIvania for her eldest son and the crown of Poland for her descendants... not the best deal but not a bad one... plus nobody can say what would happen in the election after Ferdinand’s death...
At that point, there is no union of Lublin, so even if no one can say what would happen during an election in Poland after Ferdinand's death, one could easily predict what would happen in Lithuania after Ferdinand's death. And what if John Sigismund had died like IOTL and had half-brother? To whom would Transylvania go - to his Habsburg half-brother? And main line of Habsburgs would happily ignore their cousin becoming a new prince of land which they claimed for themselves?