I believe that we cannot consider Lipinski's RO5 since it does not apply to natural product compounds. Hence, I am not sure either Veber/Egan/Ghose rules can be implemented as well
You can't leave out some products, if fulfilling the requirements. It's not blanket ban! Predicting bioavailability, in general for these cases is unachievable.
I agree with Riaz. Such compounds (macrocycles, antibiotics, etc) may be actively transported for which there are no reliable in silico models of sufficient size and chemical diverstity.