[watwut]

The end goal was world domination, as in owning whole world. So, they would eventually come to Madagascar too.

Majority of Jews killed in Hocaust were not Germans. They were from conquered countries.

So, while there was some Madagascar plans floating and while they tried to deport as many German Jews (majority of who were atheists, considered themselves Germans etc) in first stages, they were aware there is going to be showdown later on anyway.