If I understood you correctly, when you configure OWIN and therefore also Episerver AspNet identiy pipeline and call app.AddCmsAspNetIdentity(...) SQL logins are used there. Or at least users from the database that you can specify via configuration when adding CMS ASP.NET identity.
Are you looking for a way to a) adding back Sql memebership provider (assuming that it was one of the providers behind multiplex) in Owin pipeline or b) adding users created and managed by Sql memebership provider (without adding this provider to the pipeline)?
If I use Owin authentication configured in startup class is it possible to also add a MultiplexingMembershipProvider to enable an sql account login?
In documentation Owin requires membersihp and rolemanger providers to be empty in web.config