As long as matchmaking considers a console m&k player as a “pc” player then yeah native support should be added.
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essentially matchmaking is just a Filtering system, now the way destiny's Matchmaking works now is, that for PVP Matchmaking filters based on platform, in this case (PC / XBOX and Play Station), now this would of course need to be changed after the implementation of M&K support, as matchmaking would have to filter players based on input device, in this case (M&K / Controller), just as an example Call of Duty Black Ops Cold War already uses this, as it does support M&K on console.