I don't think Chronos dealt with creatures similar to Aptom before and Archanfel doesn't assume, he states that.
Archanfel's powers are so great, that he can speak telepathically with normal humans (vol.14 ch.80 pag.12-13). I'm sure he feels the the cells of the creatures around him (like Aptom does), and understands how the organisms work. Another moment is when he said to Balcus about the Relic underground in Arizona (vol.19 ch.113 pag.7-8). He understands how Aptom's body works, just by being near him (vol.6 Ch.39 pag.15) just because he was processed by the Uranus and his body is more advanced than any other Zoalord (vol.17 ch.103 pag88).