I am using a python script TOP to press the save to disk button on a rop geometry. Due to a pipeline limitation, I need to set some environment variables before pressing the button, so I can't use rop geometry TOP or rop fetch TOP.

This works, but I lose the progress updates in my output logs, is there a way to access them?

The progress updates with a percentage that are printed out are enabled by the "Use Alfred Progress" or "Alfred Style Progress" toggle on the ROP node. The ROP Geometry TOP enables that toggle automatically while the task is cooking -- in your case, you'll need to either set the parm as enabled in your script or save your scene file with the parm enabled. Most ROP nodes should have that toggle to enable progress messages in the output log.