With the new universe only having a few different trolls left, does that mean the new mother grub roxy made for kanaya will only be able to create trolls of those castes or at least those castes and the in between castes? Like, since there are no purple/indigo/fuschia/etc bloods there to provide their genetic material, would that mean there is no way to make purple/indigo/fuschia/etc. bloods?

No, we see on this page that the Mother Grub can produce trolls of differing blood color eventually.