Does it mean that instead of depending on the Visa/Mastercard duopoly you now depend on the Google/Apple duopoly?
Irony aside, yeah, this is a significant downside compared to hardware-based standards. Not so much for Android, as Google Pay and most competitors are implemented in software, but on a hypothetical iPhone or Garmin device running an open OS (don't laugh, it's a thought experiment), payment data security would be not much of a concern since all payment keys live in a secure and completely separate chip.