To clarify, there are two Ignition configs:
- The one that drives the live boot, which is embedded in the ISO image
- The one that’s written to disk by coreos-installer, if you’re running an install
Modifying #1 might be possible by re-running coreos-installer iso embed from the live system. It doesn’t make sense in the general case, of course, since CD-ROM discs can’t be rewritten at runtime. 
Modifying #2 is definitely possible. Rather than using the coreos.inst kargs, you’d use config #1 to create your own systemd service to generate an Ignition config (maybe from a template) and then run coreos-installer.