Yeah in theory if there's an upset the high seed benefits but in practice I'm not sure it matters. Especially with multiple upsets. If Montreal knocks off the Pens that's who the top seed gets so of course I'd take that, but on paper there isn't really any difference in the standings between 6 and 11 (Carolina 81 to Rangers 79). Which is why they had the tournament to the begin with.
It could be a bigger advantage in the second (and, obviously, third) round
The other x factor is that the round robin teams won't be as sharp as the qualifier teams, one can probably expect more upsets (but that's true most years anyway).