I went ahead and tried it, I guess things went as expected. Process:
copy Gemini_Dual_Boot.txt as Gemini_Dual_Boot_Rooted.txt
edit Gemini_Dual_Boot_Rooted.txt: replace "boot.img" with "patched_boot.img"
follow Flashing instructions, except that un-check all the boxes except "boot", and use Download Only option.
Flash device, boot: now it's rooted.
Can't see that I would have lost anything in the process; software and accounts remain on Android side, and Debian side seems the same also.