SP's can be registered in more than one federation but this is based on 1-to-1 agreements between the SP and the federation. Different is the registration of the SP in an inter-federation, such a eduGAIN where a given SP is "seen" by all the IdP registered in the inter-federation.
Coming to discourse.sci-gaia.eu, as soon as we will get the official Comodo certificate, we will register it as an SP of GrIDP, SWAMID and FEIDE. We could of course register it in the SAFIRE federation as well.
Once the registration is done, the WAYF service will automatically contain all the federations the SP is member of.