My InnerDrive has a WD 93048. I have a WD WD 93048-AD that I tried connecting to an InnerDrive controller, making sure the drive jumpers are the same. The formatter is GSOS. I get part way through booting GSOS when it stops. Tried a different GSOS disk. Tried to format with Copy2Plus with no luck. Also tried a WD 93028-AD drive.
The InnerDrive card is 8 bit. I’m wondering if the AD on my drives mean they’re 16 bit only. Or could the drive have a custom ROM. It’s difficult to examine the InnerDrive WD drive too closely. They didn’t plug into the drives power connector but instead the power wires come from the bottom of the power supply to the underside of the drive. Meaning that I’d have to pull the power supply and drive together. Also the WD 93048 drives have the components on the drive side of the circuitboard.
I think you're on the right track with the difference being that the drive controller is AT Attachment (16-bit) rather than XT Attachment (8-bit). XTA drives are uncommon.
AI InnerDrive uses XT-IDE drives (WD drives with X suffix). ATA drives (WD drives with A suffix) will not work with its HBA.