Is there a even a remote chance that say bits of Mammalian dna ends up in a crop via natural selection? The economic issues around GMOs are clear. The biosphere impact is not clear and there are questions: what can happen if we introduce new vectors in ecologies that have evolved over many orders of magnitude longer timelines?

The “unease” comes from the knowledge that in Nature there is always a reaction to an action. And the nature of this natural reaction (which will unfold in time, just like humans picking up agriculture) is not fully understood. It is a reasonable (read: ~substantiated) emotional response, imo.