The normal Bootleg Config works with the Steam release just as it did with the 2012 release. I re-purchased again and just tried it out. No issues so far.
It converts the game into the 1998 version though, so you'll lose all of the extra features like achievements, cloud saving, etc.
After installing it, I renamed the Bootloader as FF7_Launcher.exe while backing up the old launcher. This makes it so that you can play directly via Steam like you normally would.
The only thing that I can't figure out yet, is how to get the Steam Overlay to work when launching FF7 using the Bootloader. It works if I rename the FF7.exe as FF7_Launcher.exe and bypass the Bootloader, but then FF7Music.exe doesn't work.
Anyone have an idea on how to have the best of both worlds?