I just did some tests and actually looked through the files. It's definitely working correctly. Here's the steps I took.
Go to Tools > Firmware Configuration, click on X3G tab, and change the steps per mm values to whatever you want. When you are done, click EXPORT in the top and save the new firmware configuration with a new name (I will use "NewFirmware.frm" for this example). NOTE: This step is not optional. Because you are likely using the firmware configuration overrides in your process settings, you NEED to do this. This video explains why in more detail if you haven't done this before (
https://www.youtube.com/watch?v=NYPUAqT4UyI)
Now that you have saved the .frm file, you can click Save to exit the firmware configuration settings. Now, click "Edit Process Settings" and then go to the G-Code tab. At the bottom, make sure that the "Update firmware configuration" section is enabled and select your new firmware from the "Firmware type" list. You can click "Update Profile" if you want to use these settings as your new base profile for this printer, or just click OK if you want to test them locally without making any permanent changes (the profile saving/updating stuff is also explained in much more detail here:
https://www.youtube.com/watch?v=eZ7HFPY1wog)
At this point you are ready to go. You've created a new firmware configuration with the settings you want and you've made sure that your process will always use those new settings. Again, I have double-checked this method and it most definitely works correctly. The x3g files have the new steps/mm values applied to them, which is what the machine reads to determine how many steps to take. So if you follow the instructions, it will work
