Honestly, I have no idea. I'm not really into HD Macs. The most likely problem I encountered in those days was trying to use a non-Apple drive on a Mac which did not have the hardware capability to recognize it. The SE was the very first hard drive in a Mac and was created with a bias of only using Apple drives. It does not surprise me that the internal drives might be more problematic than the external SCSI port which had to accommodate numerous 3rd party drives prior to Apple developing their own.
I have never heard of, or used DiskManager ... Pina does not say this is the only program that may be used, but he specifically says HD SC setup will not work. DiskManager would most certainly be in the realm of vaporware today (at least a version which would work on the SE) so it is a matter of finding a copy.