IDEfix installs a new version of scsi.device. Its version number is in the range of 116+, so it is much higher than Commodore's, even if the ROM update installs version 45. Nevertheless some older versions of IDEfix do not run correctly if the ROM update is active.
I don't know what the developers thought when creating this update. But I think they knew that it does not work because it is not activated. If you install Boingbag 1 over a clean OS 3.9 installation, the startup-sequence V45.1 remains active. You get a second file called startup-sequence-3.9BB1, but it is not used unless you rename it.
If you want to use larger harddrives and CD drives on the internal IDE bus without IDEfix software, you need the ROM update. If you want to use the IDE port on the X-Surf you need the XSurfIDE driver. If you want to use both ports, you need both drivers.