I've been playing with S3D settings and sort of have it back to normal.
I suspect the same issues are what is causing all the weirdness with Cura2.
Z-offset is definitely a culprit and extrusion multiplier (material_flow) too and there seems to be something different in the machine settings between Cura/Cura2 and that's why everyone is seeing the difference. It seems these 'stock' machine settings are what the machine uses when uploading external gcode from S3D or standalone Cura or Slic3r as well.
In Cura2 Expert settings material_flow is about halfway down, alphabetically, changing it to around 102 has given me much better results when printing native from FLUX Studio.
Z-offset is at the very bottom, but it is in 2 places, once almost at the end, and then again a few lines above that. I have NOT had time to adjust and test that in FLUX Studio yet. But that will be my next test.
What I have done is add a .01 z-offset (in gcode tab) in S3D to files I had printed previously that were not printing well, and now those same files are working again.