1. You don't need the alignments for SpeciesRax. Even if you provide them, they won't be used because the SpeciesRax likelihood is computed from the gene trees only. This was indeed very unclear in the wiki.
2. There is no SpeciesRax executable. You need to use --si-strategy HYBRID to enable the species tree inference.
You are totally right about the examples, I will add several use-case examples this week, and work again on the wiki.
Thanks a lot for your questions, this will help me improving the documentation. If there is anything else, please do not hesitate.