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You can loosen the capper bell a few turns, that way it will press lower and give a tight seal on those bottles that have a shallow flange. I do this all the time on those annoying, but beautiful bottles.

I don't think there's a single easy solution to your issue with hand cappers, you may need to keep the two types around to cover as many as possible. The Bench Capper would work fine for you, just sort the bottles by height and that way when it comes to capping you won't need to change the height as frequently. There's not really a clear cap interface ...