The reason for that is Zyra's plants are a Spell and a Minion at the same time. While spells and auto attacks from other champions fizzle out and do nothing even if it's in mid air. Things like Yorick Ghouls, and Malz Minions are physical units just like plants. Because all 3 can equip repeating crossbow.
I do agree however that in a Zyra vs Zyra final unit fight the Zyra that dies first unless the remaining Zyra is then killed by the currently dead ones plants should win the fight. The only way I can advocate for it being just the first one to die is if Zyra plants become purely a spell. In which case Zyra plants should then despawn the same time she dies and not deal further damage. Unfortunately they're both spell and Minion so until then.