I don't see it as any more or less fair than a standard tournament for most teams no, the better nw players tend to get paired up with the better native players its natural just like in a 5v5 with 1 sword, this is no different apart from two of the NW players also have a sword. It is no more or less balanced than any other tournament.
With your suggestion 'If you want it to be 'fair' so you can't just run 2 Native players all the time, you can make the format more complicated:
One round you can choose whatever you like, so 2 Native and 1 NW or 2 NW and 1 Native, however, the next round you're forced to do the opposite, so let's say you ran 2 NW and 1 Native in the first round, then the next round you're forced to do 2 Native and 1 NW etc. That way you'll have to manage your team so that every member gets fair play but also makes the tournament fair with some risk & reward.'
This is harder to administrate and relies more on referees which as proven in NW most are completely incapable of reffing normally let alone with paying attention to this and remembering to administrate it. I also don't see how this is any more or less fair because it could be the same thing that 3 native friends want to play together with 1 NW guy but then they can't so you still limit players so in reality your more complicated format ends up lying out the exact same issue at a certain point.
It's not the fact that people might not play rounds if they pair themselves with lots of native players that is the issue, that's their own dumb choice just as joining an NW team where you are worse than all the players will lead you to being benched its more around the fact that the NW players that are 'okay' or 'decent' with a sword by our standards cannot face a native player with 3000+ hours in that mod and expect to do anything decent where as with 2 NW players those NW players are then given a chance to actually have an impact rather than just S key and block.