While conventional breeding speeds up the evolution of plants and skews it gradually to fit human needs, genetic engineering forces abrupt and disruptive changes in genome structure and function. The artificial gene (or edit) functions as it's designed to within the highly uniform genetic and environmental context of a modern commercial crop. How does it function in any other genome and ecosystem?
Risk assessment of GM plants has always focused on the intended artificial trait coupled to an assumption that if the altered bit of DNA 'escaped' into other plant populations it would fizzle out over time unless it conferred a clear, identifiable, risk-assessable fitness advantage. Now that we've grown GM crops in various environments for over two decades and there's been time for gene contamination incidents to inform the science, this trait-centred risk assessment is proving shaky.