The Global Settings - Stomp Select - Off doesn't stop the Bypass Assignment (or swap footswitch options) from popping up on touch, it never did that. It only stops Selecting Stomps (as the name describes) when touching the footswitch. At least that what I always remember seeing it do on my Helix Floor device.
All good here too! I used my shiny new MacBook Pro - Catalina 10.15.4, installed the new HX Edit first and then updated my Helix from version 2.82 to the new 2.90. It was fast and easy. So far all is working fine for me.