I used also HDT 2.x for some time. Silverlining was also very popular.
But I moved to later versions of Apple's hard disk setup utility (was it "HD SC Setup"? Cannot remember) - bundled with (likely) MacOS 8.5 and newer. That is the one I do recommend. Older versions (bundled with System 7.5 and before) will refuse non Apple disks. But there is a hacked version which has the restriction removed.
All these utilities will work very well on your Performa 475. It has a slightly newer SCSI-hardware (again, don't remember what it is called). In fact this is exactly what I was using around 2000 as my back-up station: A 475 with the same 14"-Trinitron-display, Asanté PDS Ethernet-card, a 2 GB external SCSI, a 1 Gig internal one (originally HDT but overwritten by an Apple driver), and finally a very reliable LaCie/Yamaha disk burner.
I was not using HFS+ for backward compatibility, so I was very happy with System 7.6.1. The Performa 475 can do HFS+ when you boot it with System 8.1. I only tried this once and found that it makes an otherwise "nippy" computer sluggish. All my disks had been partitioned to sizes not larger than 800 MB (for CD-ROM burning).
BTW: HFS+ disks on pre MacOS 8 should be showing on the desktop but are displaying only one document named "Where did all my files go?"
The Apple formatting utility you are referring to us Drive Setup. I have found that formatting a drive on a PowerPC machine causes it to not be readable on a 68k machine at boot.
if you have older, smaller drives (under 500mb), use them on older hardware (68030 or lower) and format using old third party software like SilverLining or FWB (prior to the PowerPC edition).
The change in SCSI you refer to is SCSIManager 4.3 which was introduced on 68040 Macs.
I have found that setting up a disk/drive on a newer Mac and then trying to use that disk on an older Mac can cause problems. I ran into this with Iomega Jaz disks. I had a bunch of disks with varying Mac system software versions, and I set them up and was booting and using them just fine on a Quadra 800. All of the disks were HFS not HFS+, and I had system software 7.1 through 9.0.
When I picked up a PowerPC Mac, I then started booting these disks on that Mac, because the stuff I was doing to setup drives was faster on the PPC, everything worked great. I was preparing hard drives for earlier systems and I formatted them on the PowerMac, copied over system software and then put the drives into the older Macs.
When I went to try and boot these same hard drives in the older 68k Macs, it would recognize the disk, start the Mac OS boot screen, pause for 5 seconds, and then go to flashing question disk icon. Thinking I just killed the drive, I tried booting my working Jaz disk. Same thing.
Eventually I narrowed it down to setting up the disk/drive on too new of a system, resulting in it not working on an older 68k machine.
If you have any other way to boot your LCII with the hard drive connected to that, I highly recommend you start your troubleshooting there. Boot the best OS for the machine, not the newest it can run. On an LCII, I’d recommend 7.1 just to troubleshoot. Once booted from a good disk, run SCSIProbe to see what’s going on with your SCSI chain. I can’t remember what version tells you about termination issues but 4.3 is good to use.
After your able to boot and see the drive try formatting using a third party tool described above and then copy the system folder over from your boot disk just to see if it can boot it. You can upgrade to whatever version you want to run on it later.
Post any updates back here. Hope this helps you.