I dont know what is the exact way but we only tune SQL when we find a process is slow then we just trace the session that executed the query then from trace file and tkprof we can gather the statistics and tune based on those stats, LOGGING, by default it´s set to LOGGING so all the recomemndations are actually using LOGGIN I dont know why it explicitly specified in the first but all others are using LOGGING too!

You are probably right about putting FK in the 1st column so consequently that FK is indexed thus avoid parent table blocking when simple joins are perfomed, FK will always be used as an index.. well sort of you know what mean if you know how the order of columns affects composite indexes