Multiple SQL Server instance install question for AlwaysOn
Unless you can point to the direct requirement you are referring to, I do not see any requirement in Skype for Business (SFB?) that states it has to be on a dedicated instance. 

I think what you may be referring to is the database needs to be in a dedicated Availability Group. If that is the case you can create another AG on the same instance and cluster to support your database for SFB. A given SQL Server instance can support multiple AGs and each one can have their own listener.