The rep currency is in addition to the marks, you usually get random gear or weapons from the faction you just levelled up but in this case you actually get to choose.
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•In addition to Crucible or Vanguard Marks, purchasing new Legendary items will require a Crucible or Vanguard Commendation •Commendations are received in Reputation Reward Packages delivered by the Postmaster upon reaching a new Reputation Level It doesn't say anything about choosing anything, and being over 30 in collective non-rahool rep levels for my main the commendations missed out on is very bothersome