well, in terms of the bioactivity you mention, there is tremendous bioactivity on the GI tract itself which results in a significant anti-inflammatory effect (through reducing cytokines) on the GI. the presence of cytokines in the gi and throughout the body are the result of chemicals, stress, pathogens ect. interestingly, the ability of IGF-1 to synthesize protein is impaired by a cytokine increase. cytokines also negatively impact absorption and tissue repair.
I agree with you that any peptides absorbed with be broken down into the constituent aminos. the bioactivity upon the Gi track, however, will allow bioactive proteins that are made by the body to be used for other purposes