It looks as if I used the same binary (despite the different name) for the
/system/app/Superuser piece (the file sizes and mod dates are identical.)
I used a different release of busybox, though. So the busybox my script installed would be overwritten by the glownoot busybox.
My advice is that if you want to get the google apps working, restore from a nonrooted backup and use this tool. I'm very likely to ignore my advice on my own device and see what happens, but today's not likely the day that's going to happen.
The line in glownooter that does the copy-in is:
Unless the package_extract_dir command wipes a directory before copying in the file, you'd overwrite busybox at that step but leave the links to it. The links would probably continue to work but if there's an important difference between the two busyboxes, you might find it made trouble in a weird, random way long after you'd forgotten that you'd overlaid one root with another.
The busybox updater/manager might alleviate that issue - not sure what Ed's or GD's take on overlaying one root with another is.