Every single homebrew that makes a call to the blu-ray will not initialize. Unfortunately for Gstar, just about every open manager does, as well as FTP.
When you access the PS3 through FTP (ANY! FTP homebrew server currently avaliable) you can see every storage unit present on the PS3, right? That means it'll always check to see if there's a Blu-ray present in the drive, if the drive doesn't answer the calls it'll probably be stuck in a loop, waiting for the drive to "callback".
Bottom line is, current FTP servers allow ftp access to the PS3's Drive, as long as they do that you won't be able to boot.
To test this theory (I can't remember if Snes9x emulator does tap into the Blu-ray or not but...) try downloading and running a copy of the Snes9x emulator currently around for PS3. If it runs, it's pretty much proven.