I think maybe you misunderstand the rule, it says that if there are no ALT's or LL's to replace a situation where both players in a 1st round qualy or main draw match only fail to send picks only then can a LL move into the next round, it doesn't say "what round suits the manager" or anything like that, as far as I know the final qualy round will always be the final qualy round, maybe you should ask your fellow managers about this.
You can bring the issue yourself in the managers thread if you wish - I'm quite sure the rule applies here and they'll answer so. Marto already gave his opinion above.
I'm not sure exactly what do you think should happen otherwise - no LL moving into the main draw? Bye for the 1st seed? It just wouldn't make any sense.