For those of you hitting the same issue: I found the following work-around:
BelongsToManyField::make('my relation name', 'my_relation_reference', 'App\Nova\Relation')
->canSelectAll()
->resolveUsing(function() {
return $this->relation()->exists() ? $this->relation : Relation::where('default', true)->get();
})
->required()
->rules('required', 'min:1'),
This sets it correctly on creations, while not overwriting the stored values on editing on displaying.