A loser-bracket / M-NWWC B can be run alongside the knockout stage as it is strictly independent of the main event. Basically, you ask the 11 teams which didn't make it out of the groups if they had been interested in continuing the tournament for a bit longer and you work out a format based on the numbers of nations you get.
Sure, as for everything, it asks a commitment from the captains but the whole point of that system is to give more matches for the teams complaining about not playing that many officials, so I doubt it would be an issue here.
All you need to make sure of is having enough servers to run both events at the same time. If you time things right and depending on the amount of team you get for your M-NWWC B, your secondary tournament would finish one or two weeks after the main event. If there are nations which would enjoy that opportunity, then I would say to go for it, and if motivation/time in an issue on your side, then I'm more than glad to help you out.