I meant the internal controllers provided with scsi.device in kickstart, like A600, A1200, A4000, A3000, A4000T and I have probably forgotten some. Those are mainly the reason why there are different kickstarts in the first place.
You are correct.
The SCSI "scsi.device" versions in the A3000 and A4000T ROMs are built to assume that the hardware required for SCSI operations (DMA controller, WD or NCR SCSI chip, respectively) is present. This built-in hardware is not placed in AutoConfig space.
The IDE "scsi.device" present in the A600HD, A1200HD and A4000/A4000T can auto-detect the presence of the required Gayle/Gary hardware, which as far as I know is not a given for the A3000/A4000T specific SCSI hardware.
The other reason why there are ROMs specific to the A3000 and A4000 models is in that the RAM controller (Ramsey) may have to be asked to support page mode for the peculiar type of DRAM that may be installed in these machines. As far as I can tell this does not seem to be necessary, though. Support for page mode (also called "static column mode") was intended to improve DRAM performance on the A3000, using the 68030 under certain circumstances. In practice the gains were not as significant. If I read my A3000T service manual correctly, Ramsey should boot with safe defaults, which makes switching to page mode unnecessary; it's also quite difficult to do without crashing, because you have to fiddle with the Ramsey configuration while not running afoul of ongoing DRAM refresh and other flaming hoops to jump through.
Finally, different types of ROMs are required by different machines, with respect to where the kernel is to look for ROMTags, how much stack space it may use, etc. If I remember correctly, the big difference here is between the machines built around the architecture of the A3000 (which includes the A4000 and A1200 models) and those which precede it (this being the A2000 and the A500; I think the A600 belongs here, too).
In a nutshell, if you're going to bootstrap the system, from the bare metal, in a real Amiga, then you will have a devil of a time getting the basic three "scsi.device" variations to work together in ROM: one of them will always crash.