The CM choke or Balun can go anywhere in series , as long as the wire pair are closely coupled. e.g. twisted pair.
The purpose of a CM choke is to raise the CM impedance and then shunt CM voltage to ground to reduce interference in either direction. Design depends on frequency and current spectrum of differential signals and CM noise. In some case line filters may use two stages for handling a wider spectrum. Ferrite clamshell sleeves or torroids with lossy ferrite raise impedance and absorb RF CM current noise in DC chargers (optional), every VGA cable (mandatory). Often DC chargers are still excessive in CM noise for external mics and other instruments. telephones and Ethernet PHY ports all have Baluns to improve CMRR not possible by active means.
Baluns help reduce noise ingress or egress ( radiated and conducted). Depending on specs. isolated converters may use this to reduce conducted/radiated emissions on primary and/or radiated emissions on secondary.