Yes I would exclude the odd person to avoid the unfair bye point system.
So you get why no store is ever going to tell someone who's travelled from wherever carting their X-Wing kit "sorry, you can't play today because it's marginally unfair to give one random player a first-round bye? Thanks for coming! If you've enjoyed your visit please tell your friends!"
It's spending an afternoon pushing plastic ships around a mat in the hope of winning within-a-rounding-error-of nothing. It's the lowest flippin' stakes imaginable. This feels like a weird hill to choose to die on.